The runes allow for more complex building already. The problem lies in the balance; currently, the runes have a few really good sets per type, and then everything else is trash.
With Marks, it's generally offensive stats like AS, AD, AP, ArPen, MPen and Crit that are worth having.
On Seals, Armor is most common, and then some also use HP or HP/lvl, haven't known any others to be very efficient.
The Glyphs are pretty much always MR, Mana or CDR, either flat or per-level depending on the user's preference.
Quintessences are much closer to balanced, there are few sets of them that are not worth using ever.
Still waiting for them to overhaul the balance in the rune system...