Let me see if I can clear some things up here...

HB, you need to read the Advice Needed thread I started last week to get info on the historical makeup of the medieval armies of each faction. It's probably on page 2 now. It explains a lot of where this list comes from, plus I give some other explanations of my aims with the mod.
A lot of the questions you raised are answered or cleared up in that thread, though YP did a good job with several of them.

My thoughts on unit use:

From my experiences, which I admit may not be as extensive as many of your's, the AI does ok with Sp. Jinettes. It's the infantry that they can't use, because it can be ridden down by faster infantry or cavalry. The jav-cav units (jav-cav is a unit from my other medmods) are meant to be hobilar-like scouts. They aren't *supposed* to engage other units head-to-head, so even if they didn't have the javs, I would want them to avoid engagement if possible.
The times when I have tried to chase down Jinettes, I have simply winded my Mtd. Sgts or knights, left their backs exposed to the other AI cav units, and trapped behind their lines.
I frequently use my light cav as bait versus the AI, so if we want to pull off one or more of our units to chase them down, that's our mistake to make, as far as I am concerned. They are to be used to run down fleeing infantry and/or cav units, and if they can launch a few javs before then, then that's an extra benefit.

I think I will go ahead and remove the jav infantry unit from the generic list. I just thought of them as being shirmishers available to fill out a main army in the Early era, or a non-homeland garrison in the later eras. They may be more trouble than they are worth if the AI loads up on them as soon as they are available, and before it has access to better troops.
I hope to use the minor factions concept, where there will be *no* rebel provinces at the start of the game, to eliminate or tone down the AI tendency to load up on whatever troops are available as soon as the game starts. I believe that it does this in reaction to the over-strength rebel provinces on its borders, so that by making them real factions, it will remove this reaction, among other game benefits.

Morale:
CA gave all units in the game 2 more morale points for the expansion, in response to player calls, mostly MP'ers from what I have heard. I plan to remove these added points for the generic units and the HRE units. I plan to remove them from the HRE units to reflect the reality of the Empire's fragmented status. This balances out the fact that the HRE has no holes in its unit lineup.

Gallowglasses:
From what I have read, in more than one place, they didn't appear in battlefield reports until circa 1250, fighting with the Irish. I didn't hear that they were mercs, so YP would seem to have more in-depth knowledge of them than I, but I want them to be a Ireland-only unit, like in 1.1, available to the English after they take over the heart of Ireland for the High era.
I agree with YP in thinking that CA pretty much mythified their explanation for putting glasses in the VC. *I* believe that they were included to give the Irish one unit that didn't absolutely SUCK when the AI was in charge. I am going to try and give them another with my last VC update, btw.

I had actually forgotten about Highlanders, but I will leave them alone, so the English can recruit them if they conquer Scotland.

Generic units:
Arbs fall into the bolt category with X-bows, so they will be available as before. I meant to convey the thought that all the "standard" projectile units, from Archers to Arquebusiers, will be available as before.
You can include the artillery in with that as well.

Militia units:
From what I keep reading and hearing from posters, militia units, or levies, were spearmen, not axemen. Again, I would take your historical examples that contradict this into consideration, but what I keep finding time and again is that, outside of dismounted knights, blades and polearms were rare until you get into the late era in the north, and were secondary weapons to the bow most everywhere else.
Btw, cav units will dismount into the same units as in v1.84, unless a special circumstance is present.

Swordsmen:
Please see militia comment above.

Non-Homeland troop availability:
I want you to be able to raise basic, early-era level troops in these conquered provinces, along with missile and artillery units.
Special units like Flemish Pikemen or Lithuanian Cav may be built under certain circumstances in selected provinces, but basically the heart of the Homeland concept is that the quality troops needed to defend all of your provinces will have to come from your ethnic population.

Faction holes:
I really don't think I have left many gaping holes in the faction lineups, unless you want to talk about unit types unsuited to their native terrain.
For factions like the English who may need swordsmen in the early period- this is what the buildable mercs are for. The building priorities will be set so that the English build the required structures for Viking Landsmenn, and the AI should start spitting them out. The English won't have a lot of them, but they are only supposed to have enough to defend with, not attack. If they want to attack, they will have to develop their faction strengths.
The English, for example get their best units in the high period, when they can perhaps weaken the French. The French were indeed weak at the start of the Hundred Years' War, and will be in the mod with the emergence of Burgundy. However, the French then receive their best units, with which they can, perhaps, turn the tide.

Statistical differences:
Unless noted, new units will have exactly the same stats as the old units they are compared to in the unit lineup. They will also have the same icon and same battlefield look, so we won't get bogged down in learning a whole new, very long unit list.

I want them to have their historical names, and I hope some of you will volunteer to research and write accurate, historical descriptions for them. Stuff like this is what makes a game come *alive* (those of you who have played previous medmods can perhaps attest to this), and really immerses you in the time and place. In my other mods, I needed a half-dozen people just to help with all the descriptions, and I am going to need some big-time help with this one as well.

Danes:
I am getting away from historical accuracy with their lineup to some extent, but for gameplay aspects I think that there needs to be *one* Catholic faction whose strength is infantry.
I want each faction to be unique, and I prefer to have one faction specialize in each unit category, so that we get the opportunity to experience a full variety of situations and challanges on both the strategic and tactical level.
My thinking is that the Danes will be well suited to rainy, cold and forested Scandinavia, but they will face increasing hardships if they try to expand too far south or east. Their hardy axemen should do well versus knights until perhaps the late era, when they see the need for a type of Gothic knight to better defend against the advanced units of the French and HRE. They can protect against flanking attacks, and force the enemy to engage in melee, when the Arm. Huscarles can chop them to pieces.
However, if the Danes go a'Viking too far from home, and see a horde of Mongol HA's surrounding them on the Steppes, they may be screwed.

This leads into what the whole mod is about-

1)Every faction is distinct and unique, both to play as and to engage in battle. I mean, you could play Custom Battles and get up to 30x30 unique challenges just playing in the same era and on the same map.
2)It should be a bitch-and-a-half to get a complete conquest victory, or even a partial one if you start in the Late era.
Also, from the way the units are shaping up, the Late era appears to be the most interesting one, which is significantly different from what most people report with the current setup. Perhaps we can get into using Serpentines and assaulting Fortresses. Wouldn't that be...Medieval?
3)The game will give a much greater historical feel than before, both from 1) and 2), and from the historically accurate names, abilities and descriptions.
Right now, I plan on calling this version
The Medieval Mod IV: 3D - Feel it, Play it, LIVE it.

(Just don't ask about diplomacy, though that part will be a little better too with the minor factions concept.);)

Will it all work? We'll see, but if you're not stoked just from reading my two posts in this thread, then you need to go back to playing chess. THIS is the stuff that gets *me* stoked about mod-making, and THIS is the stuff that the Medieval Modification Packs name is all about. Up until now, I have been learning about the game and the era, and tuning things up. Now we are finally getting into a complete overhaul, at least with what we have access to, and this is the stuff that has resulted in players like you sending me checks for up to $40 once when I asked for donations that reflected the mod's worth to them. (I asked for the donations because I was facing a potential crisis with some upcoming medical bills, but that didn't affect their donation amount.)

Making these mods has been a blast for me, and so too I believe for everyone who has helped with them in the past. I hope some of you join in on this one, and we can get that feeling once again.