I've a feeling that you get the intermediate upgrades bundled with the next major upgrade, so I doubt you'll end up missing any structures.

Having said that, you don't get any corresponding price reduction on the next level of castle build, if you did build the intermediates.

Convoluted way of saying that you save time and money by not bothering with them. But read on...

I'd suggest that you build your first keep without doing the intermediates, since this lets you build the swordsmith and other keep-dependent buildings and upgrades a couple of years earlier.

At other locations where money is not a problem and there's no particular urgency in progressing the local tech level, it is worth spending 200 florins and 2 extra years on motte, motte/bailey in several locations as it will help give your faction leader the 'builder' V&V, which boosts province happiness empire-wide. Later on, individual govenors will get builder virtue as well, for a further, local, boost.
Total number of constructions seems to count towards gaining this, rather than amount of money spent.

When the king eventually dies, you lose the builder happiness boost and his successor lacks the virtue, so it can pay to postpone some cheap/quick constructions and then have a sudden burst of building just after he has come to the throne.

In terms of tactical battles, the maps are changed by the builds.
+motte gives your archers an elevated area and, now they have line of sight to a target outside, they can fire over the stockade without difficulty. Without it, sometimes they don't fire when you tell them too.
+bailey adds an extra enclosure to the wooden stockade of the base level fort. Attacker has to capture both enclosures to win and it takes meticulous catapult placement to be able to breach both enclosures with just one unit. (Don't bother with the gate(s), just smash the walls).

Keep + curtain wall is useful - again a second enclosure - only a 2 year build and you have that extra protection during the 10 years it will take to complete the next castle up.

I can't answer about ballistas etc retained after you add cannons. Common sense says its replacement, not both of them together but you never know...

HTH