You can disable pretty much every 1.13 feature you don't like. There's no reason not to use it unless you are a purist.
It adds so much that at least 1 purist playthrough beforehand is encouraged. 1.13 pretty much can make JA2 into a different game.
I remember being very annoyed by the 100AP system of 1.13, coming from original's 25. So it might be a good idea to make a minimal 1.13 config anyway, just to be getting used to the numbers. Every action taking 4 times as much AP as before feels very wrong for some time.
I think 1.13 could use a setup tool that would guide the player through the most important INI settings, like counterattacks, max.number of enemies in sector at once, economy, etc. You can turn the game into a blitzkrieg or prolonged war of attrition, redshirt flood or sparse elite opposition, or even start the game as if it was already endgame in most respects.
The INI editor is pretty good, but the options are overwhelming for a newcommer. I don't think many people finished their first 1.13 game without reconfiguring and restarting at some point.
Overheating feature is pretty great, as it gives machineguns their proper edge at sustained fire. Not so fond on dirt & cleaning, as that one just adds busywork and an item to carry. And I like to bump explosives damage to 200%, all explosions ,maybe except for mortars, feel too weak at default. Well, I have never been near an exploding grenade, but I don't think I'd just get knocked over and bruised.
I really like what they did with the inventory and guns. The amount of weapons and attachments moved it from vanilla's linear climb with "tickboxes" to search for compatibility and usability. Range stat is no longer the only real distinction of quality, so the duct-taped barrel extender is just a temporary half-assery and gets replaced by suppressor or muzzle break on good guns. You can pick your scope depending on how much versatility and sharpshooting you need, with tunnel vision and aiming speed and all that jazz.
No other game has me looking for a "not too heavy rifle with effective range around 400m that can take a 4-6x scope, a suppressor + subsonic ammo in stock, preferably of a common caliber".
Damn, gotta install JA2 once again, soon.
Have they reimplemented the pre-seeded RNG from vanilla? I liked how it forced me to try something different during my turn and not just reload the shit out of my 5% hit chance to save my skin in a pinch.