Yes, the version to get is the 1946 at the moment, it still has official patches being developed for it and tons of user-created content.
As for choice of mods, I would recommend starting with updating the game to its latest version (4.12.2m) and then installing either SAS ModAct 5.3 or HSFX 7.
If you plan on doing mostly single player, go for HSFX 7. If you plan on flying on multiplayer servers, well, it depends on what servers you're flying on. If you want to fly on stock servers, either keep the game stock or install SAS ModAct. If you want to fly on servers that use the exclusive features of HSFX (such as more realistic flight models for some planes), you'll need to install HSFX for obvious reasons.
UltraPack 3 is another option but it's getting outdated, doesn't support the latest patches (so it's already lagging behind on features) and, as far as I can see, doesn't have as much support on multiplayer servers.
Also, you might feel that it's unnecessary waste of HDD space to keep unmodded, stock versions of the game around. It isn't. Every time the patch rumba starts, you'll need to install new official patches on top of clean game configuration - this game's moddability is not as simple as with FS2 Open, it's a lot more messy. Installing mods? Works fine. Uninstalling a mod pack to return the game to complete stock configuration? Not so easily done, and most of the time not worth the trouble - it's easier to make sure the game is really stock version by re-installing it, than to make sure you've gotten rid of all the relevant files that a mod pack had added in.
So whatever you do - best way to keep your game stable is to always install things on top of a stock game.
You can probably guess that I'll give a recommendation for this game as well. It has reasonable graphics, although the limitations of the engine are becoming more obvious compared to new titles. It has good performance, being a pretty old game all you really need to run it is a mid-range modern GPU (anything past GeForce 8000 series will do just fine with this game) and a CPU with good single-core performance. If you want to do other stuff like use FreeTrack or FRAPS/DXTORY/OBS while flying, then you need some more oomph (as always).
My opinion is that using this game for single player is a waste of potential. The AI is now better than it used to be, but on the other hand it now pulls some ridiculous stunts like shooting at your with precise aim even though you're clearly behind the enemy pilot's engine cowlings (in multiplayer with closed cockpits, you can actually look at the enemy plane and estimate whether they can see you or not...).
Also, doing static campaigns has novelty value (flying some of the more exotic planes on less well known frontiers), but you probably don't want to fly those more than once if even that.
Dynamic campaigns are an endless series of very similar missions where, depending on the campaign settings, you can spend most of your flight time in transit even with time acceleration (which only goes up to 8x). There are some systems which actually make campaign missions dynamically so that there's some level of persistence and your efforts can affect the course of "war", but even so I don't really see the appeal of doing single-player missions against AI.
Multiplayer Co-Op mode against AI is another thing altogether; although with same system you can just as well have multiplayer team vs team co-op AND dogfight matches.
The game has two multiplayer modes: Dogfight is more popular, Co-Op is more sophisticated and usually used for more realistic missions. Dogfight missions allow re-spawns and are thus much easier to organize. Co-Operative mode gives you one life, one aircraft - if you die or crash, you won't get another. The advantage of Co-Op mode is that you can do stuff like multi-crew bombers.
DF matches are more open-ended random dogfights although nothing prevents you from teaming up with other pilots, and designing a mission goal to complete. Some servers encourage this behaviour more than others.
COOP matches tend to be more mission goal oriented although there's no gameplay mechanisms that force players to do any single thing, so the individual pilots have to stay focused on the mission and not go chasing enemy fighters, for example.
I am an admin at Skies~of~Valor, which is the server I spend most of my IL-2 flying time in. It is a server with a sort of middle ground of realism. All the flight model oriented difficulty modes are enabled, but while we use closed cockpit setting, we allow use of external views. Server is running stock game but allows joining with modded game client, as long as it doesn't modify the flight models or weapon damage or such things.
The server lives on a collaborative server with another popular server (Warclouds), though we have a little site of our own. We offer stats tracking for each month at a time, then the stats are reset (barring technical issues that sometimes force us to reset stats earlier).
You're all welcome to join there.
War Thunder... well... you'll probably find that most IL-2 pilots have a pretty clear opinion on that game.
Honestly speaking though, it clearly isn't even designed to compete with IL-2, its appeal is mostly on a different crowd. Aside from splendid graphics, War Thunder in its current state has nothing to offer to experienced IL-2 pilots - they would need to completely fix the Full Real mode and make more planes immediately accessible on Full Real mode; the Grind to gain planes really isn't very appealing idea to me at all.