RTR 6.2 includes Darth's formations (Darth is now on the RTR team), although Darth also has his own game which is closer to vanilla RTW than RTR.

Most mods are mutually exclusive, so I am content with RTR alone but am currently playing BI with the bug-fixer (made a copy of RTW so I can have both RTR and BI on my computer). RTR is a pretty amazing mod IMO - it makes the units more historical (and more aesthetically pleasing), it re-balances the combat (cav, missiles and infantry) in a way that improves gameplay and realism, and it slows down combat to make it more immersive and less chaotic. It also has a nice system of "areas of recruitment" that prevents you quickly raising armies in newly occupied lands, as well as providing a lot of interesting auxiliaries.

EB promises to do similar stuff, with perhaps a more in-depth focus on the history and looks gorgeous, but they sure are keeping us waiting.

But I'm not sure any mod will really solve the problem you have about the difficulty level. RTR slows you down and beefs up the opposition, but still can be easy as some factions. You might try some house rules to up the challenge, eg:
(1) only take max 10 units per stack
(2) take historically balanced armies, not just the best units
(3) never retrain any units (just merge depleted ones)
(4) never exterminate a city
Obviously, play on VH (at least campaign, VH battles just does not feel right to me).