Brigade E5 is a JA2 clone but with a far smaller and dumbed down map, both strategic and in sectors: there are few enterable buildings, not to mention the inexistance of cool dungeons, secret bases, caves and everything else that made the JA2 so wild, varied, large and fun.
A follow-up to Brigade E5 is in the works:
7.62
While it will look better than E5, neither of these can come close to the gameplay of JA2. The only problem with that game is the crappy graphics, but it's definitely the best squad-based game to this date, though perhaps tied to the first two X-Com games.