I would go for this on your first run-through with (I'd recommend) Seyfert, and cross-reference the guide here by this fellow while going after Moon Traveler (visit ALL areas) and collect 50 MCs while doing so. I opened the MC location guide in one tab and the the area checklist/flow guide in another tab and rigorously picked up every MC and visisted every area first time thru. No reason to try to pick up some MC's here and there with one character and then others with another if you are going for Moon Traveler, because you have to be quite methodical not to miss any areas, and really there are only about 6 or 7 MC's that are useful at all, and most situations only require between 4 and 5 different types, so if you are going for Level Maniac there's no need to pick up tons of MC's on your other characters.http://www.ps3trophies.org/forum/moon-diver/102813-moon-dive...
Follow this guide's directions for visiting all areas from top to bottom- he re-lists them if you have to start the stage over to hit all the areas. I would open up the level/split-path/secret area guide on one tab/window and the MC location by area in another tab and constantly cross-reference them as you progress through with your first character (I'd recommend Seyfert and dropping points into POW until you can kill the yellow exploding enemies with a regular attack without Frezo's atk increase MC on easy, but you'll need plenty of HP and a decent MP pool to survive the laser cannon heavy stages. Use Niltor's Chorus or others in that line to deal with those- they are are practically mandatory to survive(these are the "freeze all enemies for x seconds" MC's).
By level 60 my seyfert was well-balanced to handle most stuff with about +19hp, +16mp, and +20pow, although early on I was dropping more into pow, and later more into mp, because you end up needing to use Niltor's freeze MC's a lot, and you are going to get tagged by lasers and they hurt like hell, so you are going to be casting Ceno's heal MC's quite a lot too. Stick to the 2p Ceno's MC once you get it, unless you're playing Hitori and have MP to spare- it's more efficient than the 3p.
Once you get through the game on your first playthrough with Seyfert (which most people recommend), you should have collected all the MC's and gotten Moon Traveler achievement for visiting all areas. And now if you are going for 100% completion you can rush through the stages with the other characters and only go out of your way to pick up particularly useful MC's like Niltor's etc. The first run, making sure you hit alllllll the gobs of side-paths and secret areas will take quite a while, but if you don't follow the guide posted above to the letter, you are going to be left wondering what area you missed for Moon Traveler (visit all areas), and that one should be done at the same time as collecting 50 of the 60 total MCs IMO.