What runes would I like to see.. more ability runes. Suikoden 2 had it right, plenty of characters had unique runes and it gave them personality.
I agree, since Kika and Mizuki are going to be in this game, then Konami might as well give them their Falcon and Shrike runes as well. For other charcters, Kyril could have his own ability rune (not a migcal rune) and use that for a special attack.
Other than that, everything Stallion said.