Both JA+ and JA++ offer SP and MP systems.
Base only offers SP.
JA+ tweaked the damages, collisions and block/parry behaviour forcefully. JA++ also tweaks some of those things in a less retarded way which you can activate with japp_saberSystem 1 - this is not an alternative to SP/MP, it works in tandem with that setting (d_saberSPStyleDamage 0-1)
As for what JA++ is lacking, the only major thing I can think of is full-force duels and alternate dimension. I'm hesitant on adding alternate dimension because I think that's a bad way to handle the whole laming (so-called) problem.
Anything else that's missing, I would be happy to receive reports on so I can add it with haste. That's the real benefit of using JA++; if you want something, you get it.