I Dont know why you dont see them, unless your not living long enough, because they continue to appear. I just beat the game two nights ago, and it is tough. The only attack he uses is the energy wave, just do a double jump to avoid that, he leaves a puddle of phazon after 4 or 5 shots of the energy wave, so once you find him concentrate on avoiding his attack until he leaves a puddle, the problem is finding him because you have to use three of your visors, you dont use the scan visor, and while your looking for him, he and the smaller metroids are beating the crap out of you. Use the power bomb to get rid of the small metroids before you try to attack Prime or they will punish you. There is another form of small metroid that shows up when you get close to defeating Prime, they have a beam that draws you to them, turn into the ball and boost away from them, kill them with a bomb or the phazon cannon. You want to try and have most of your life left after you beat the first form of Prime, because you definitly need it. Like I said it is a tough fight, but I did it on my third try, just keep at it you'll get him. I hope this helps. Good luck.
TOY