No matter what you choose, sometimes make sure to get the per level runes over the flat runes. You get double their worth at level 18 and more than the flat rate after level 10.
It depends on the champ (and overall matchup). Someone who has a weak early game + strong lategame like Yi or Olaf, doesn't benefit much from per-level runes as they'll still start 0-5 and try to climb to 37-6 as the game passes 45 minutes. If they got Flat runes, that would make their first few levels much less painful, hopefully making them 2-3, which gives them the money and XP to start owning faces at 25 minutes instead of 45. Junglers also (used to much more so) want the flat runes, because they are dealing and taking damage constantly starting from level 1, rather than safely last-hitting for the first 10 minutes.
For Morg I would consider:
Red: Magic pen, no question.
Yellow: MP5/level is great. If you buy a lot of mana items (or you expect to get jumped on a lot by Talon and run out of life before you run out of mana), Armor/level could work instead.
Blue: AP/level works, Flat Cooldown Reduction (the per levels don't pass flat until about level 13 iirc, and the extra fraction of a percent won't affect what items you buy to reach 40%), Resist (flat or per level) works.
Quints: AP (flat or per level) is nice, moreso than Magic Pen or Spellvamp imo because it affects Black Shield. Flat health or Movespeed are decent on any character.
Blitz:
Red: the new Destruction hybrid runes should be fantastic, since blitz always does some of both damage types. The magic pen from morg isn't bad if you want to save money (and likewise, she'd do fine with the hybrids as well; heck you could buy 4-5 of each and grow them to 9each over the next decade if you want)
Yellow: MP5/level works, Armor/level works.
Blue: Flat Cooldown Reduction probably gets the nod so you can hook from the bushes more early game (and spam Power Fist and Ult more later). AP/level, Resist (flat or per level) work too.
Quints: Destruction if you like doing damage with blitz. If you prefer getting assists by spamming grabs/knockups/silences, might prefer Movespeed or more Cooldown Reduction (Power Fist with 40% CDR is fantastic!). AP or Flat Health can work, as can AD (but that wouldn't really overlap with Morg, and I think the Destruction would probably be better anyway).