So far the Acekard looks to be the hands down winner for NDS rom compatibilty, and the hands down loser for ease of use.
The manager is simply the program you use to patch the roms to work on the cart. All slot 2 carts need the roms to be patched AFAIK. The G6 manager (the only one I've used) is easy to use and has some nice features like rom trimming & soft reset.
The DS-X runs clean (unpatched) roms so it doesn't need a manager; you just copy the file to the card. The Acekard also runs clean roms but it has a funky filesystem so you have to use their (currently very buggy and feature-free) software to transfer the games.
imo, acekard has the biggest potential so far, it's easier to improve the buggy client than to fix every single problem on ds games (ds-x, ninjapass x9)
but we have a microninja to look forward to (reviwed soon hopefully),
and also supercard and m3's version on slot 1 solution, who knows when these came out
as for me, currently i have 2 ds-es, 1 ds phat for me, and i bought a new dslite and i gave my m3 mini sd for my bro
i'm looking for a perfect solution to give him on his dsl and i'll just use the m3 mini sd, so far i'm keeping an eye on acekard
on slot 2 solution, it's impossible to run games without patching, so 100% compatibility without updates are almost impossible, so i'm looking for a slot 1 solution, once acekard has proven their client update support, i'll get it