The most comprehensive systems for converting those games would be using Hero System or GURPS because they are toolkits where just about every rule or situation is covered. However, that being said, it involves work.
Of course, with any crpg, you're going to have to put in a lot of work to deal with all the myriad mechanics to adapt it to any system; otherwise it won't feel like the game you're emulating it will just feel like d20 or some other system with anime in it.
With these crpg's though, there's a couple of issues to consider as well:
1. The power levels have numbers that go into the thousands that you have to think how rolling dice will be beneficial. Some of these games start you off at 100+hp at 1st level and when you get to 20th level or whichever level is the cap, you're at 9,999 hp (or more). So if you adapt a game system to emulate all the power damage and scaling, there's little point in having a longsword that does 1d8 points of damage when it's modifier is +5000. Anima addresses this with weapons doing base damage (no rolling) and depending upon your skill level and success level, you can go up to 400% damage from your weapon (I think, it's been a while since I looked at that game).
2. The power scale vastly differs and affects campaign play. In these crpg, if you play above level, you get killed, the fights are just too hard because monsters do way more damage than you have hp. This makes the games fairly linear in that if you're given Choice A or Choice B, the logical step is to take Choice A, because Choice B will kill you outright. What does this mean for table top play? That as GM, you have to really structure campaign play so that the encounters fit the levels. You'll need mechanics that groups all objects by "level" so that a group of 15th level characters wielding 15th level magic weapons and items can defeat a 15th level monster, but will be obliterated should they face off against a 20th level monster and that monsters who are 10th level or lower have 0 chance of success. This can lead to play-style issues of having to create balanced encounters. 4e emulates these mechanics in which you can have level appropriate monsters, parties, and magic bling for balanced encounters.
I think the easiest way is to build your own set of mechanics but use the game guides as most of your work. For example, when you go out and buy and Final Fantasy game guide, it lists all the weapons, their damage, monsters, their hp damage, etc. Then it's a matter of "filling in the gaps" and determining how dice rolls will work, character generation, etc. For example if you have a longsword in the game that does 500 points of damage and you want players to be able to roll some kind of variable damage, you can choose a simple 1d6 roll.
1 - 50%
2 - 5 100%
6 - 200%
If you want to make it more complex, then scale the dice to 3d6 or 1d20 or 1d100 and create a table that does more variable damage. The problem with this is the math component. But what this does is allow you to use the crpgs scale of power which will emulate the feel of the game most closely.
Or you can say that you just want the "flavor", but not the actual numbers. Then you can choose a system of your choice that's expedient for you, but just scale everything down to whatever mechanics the system uses. Instead of that magical longsword that does 500 points of damage, it's just a +3 longsword if I'm using d20. My hunter class is going to be the fighter class, the ranger class will use ranger without the spells, and my forces class is the wizard / sorcerer / cleric.
