I started running an ongoing MF game a couple months back, and my players just hit level 2. After taking a look at the relatively spartan return for reaching the next level, we decided to sweeten the pot a little bit, and provide some control over character/skill development. Here's what we came up with.
When a character levels up, they get:
-+1d to their hp (except androids; they stay at 50hp); mutants get an additional d6, pure humans get an additional d8 to their hp.
-Whatever they roll on the "Experience Level Bonuses" chart, but with one change: should they get a +1 to an ability, they get to choose the stat they want to develop.
-The character gets to choose a mutation to develop. By and large, this would entail some further ground-ruling/negotiation as to the terms of that development, but the quick-and-dirty idea is that development of beneficial mutations would improve by 1d (I sort of used the ideas covered in Mutant Omega concerning 'mutation points' et al), and detrimental mutations would halve.
For example, a mutant has the Mind Thrust mutation and chooses to develop it when he reaches Level 2. He can choose to either have the mutation do more damage (by an additional 1d6) or increase the range of the thrust by an additional 10' radius.
Another example: Mutant B suffers from Phantasmal Damage, which doubles all damage taken. When he levels up, he chooses to develop this mutation, which will halve the effects (i.e., 150% damage instead of 200% damage). Should he choose to develop the mutation again the next time he levels up, THOSE effects would be halved (i.e., 125% instead of 150%). If he chooses to develop the mutation still again, its damage effects would be rendered obsolete, though he still might, say, distantly recall the negative vibes that used to cause that extra damage.
That's what we've decided to do. If anyone else has added bits to the level-up process, I'd be interested in modifying my current game to include them, as we're still early on in the adventure.