Which one do you guys prefer?

Of those two?

MP5/level, because they are amazing while cdr/level glyphs are average at best.

Get flat CDR glyphs if you are gonna get CDR glyphs.

CDR/level are useless so MP5/level is the better choice. Flat CDR is better than both though on most champions.

It depends on the champions really, I would much rather having MP/5 per level for say Ezreal or Anivia. However CDR runes should be a mix, all flat won't give you enough to get 40% with certain builds, while per level give too much but not early enough. I think someone did the math and it was 6 flat and 3 per level for CDR glyphs.

I do mp5/lvl seals and CDR/lvl glyphs

It depends on the character. CDR/level are only good if you are looking for mid/late game 40% CDR through items. Mainly support characters who don't have mana issues late game, but are mana limited early game.

MP5/level glyphs I use if I'm wanting armor in my seals and I want mana regen to not be an issue after level 6 or so.