I'd agree that most games tend to trail off lategame, but I'd say that the earlygame of JA2 has its own problem, and it's the midgame where things really shine. Lategame you have tanks and bullshit scripted 'ambushes' where a soldier will sit in a corner behind a door forever until you walk into his field of view and take a near-unavoidable burst to the head, plus scope issues. But earlygame you have poor gun variety and 'by rote' combats. As someone who plays the game Ironman-style (not the 'can't save in combat' way the game defines it, but in the 'Only save/load when you're turning it off/on' way), I'd really find the earlygame much improved if the liberation of Omerta and Drassen were some kind of skippable tutorial, because it's easy and there's little variety to it.
Not that I'm shitting on JA2 - it's probably the game I'd take with me on a desert island - but it's the midgame where it becomes something special, when you're desperately spamming grenades and trying your luck with mortars and LAWS to push back 20+ elites who are overunning your position. Or when you're forced into an assault on Cambria or Alma that you're not ready for because you dicked around and the Drassen mine just ran out of ore and you spent all your cash at Bobby Ray's.
Pretty much everything after Drassen/San Mona and before Meduna is gold. Though I'd kill for some way to automate the 'Search all the lockers/chests/drawers and talk to the NPCs' stuff after the battles are done.