I definitely don't like Zilean's current passive, being a mid Zilean player. However, your proposed change would effectively force Zilean to build mana (rather than mana regeneration; ex: Seraph's Embrace over Athene's Unholy Grail), and Chronoshift doesn't need a buff (it's probably the largest chunk of Zilean's power budget, and it's already on an extremely low cooldown). Zilean's current passive strongly encourages him to support because he can double the benefits of his passive (extra experience for two champions); yours would strongly encourage him to build mana items. He doesn't need his build paths to be constricted, just like he doesn't need his choice of lane to be constricted.
I think the main problem with new Zilean is that his bombs' "sticky radius" is a bit too small for the delay in throwing it + a second bomb's target prioritization seems buggy (this may be due to the sticky radius being so tiny).
As for a new passive... I would be satisfied if Zilean's current passive simply gave a larger XP bonus if it affects fewer allied champions at once (more for Zilean if he's alone; less for each ally in the AOE if he's with friends). Although, that would still be a dull, non-interactive, invisible-power passive that doesn't really explore Zilean's "time mage" theme. I'd prefer some sort of minigame... Perhaps if Zilean puts his bombs or speed boost on an ally, he decreases their cooldowns, but if he puts his bombs or slow on an enemy, he increases their cooldowns. If that is too strong, it could be changed so that he has to "doubletap" allies or enemies in order to affect their cooldowns (two bombs or speedboosts, maybe a combination of one of each); it could also be changed so that it doesn't affect ultimates.