I actually had a draft of a Zilean rework laying around in my Docs... so here goes nothing. I'm gonna discover its content at the same time as you (technically, a bit sooner, since I have to reread to to complete it and make sure I agree with myself).
Theme : Support-over-time
Pros : CDR, Regeneration.
Cons : Low offensive capabilities, Low burst resistance
Right now, Zilean has a few major problems. First of all, his playability at various level is shaky at best. For low level players, the fact that his bombs are undodgeable, deal quite a bit of damage and deal AoE damage makes him terrifying. At higher level, his massive needs of mana, as well as low base high scaling on ult and his little "instant impact"/playmaking makes him a very secondary support option. In my mind, he can be compared to Poppy Top, it works, but other options are much better (but it still works wonder in unintended positions).
Next, his gameplay ages badly (sorry for the pun). Basically, the way to play him is ENTIRELY different based on the game phase you’re in. Early on, you poke with bombs and rewind, come mid game, you simply allow for revives and counter-initiates, and late game, you are there mainly to peel with your slow since your bombs now deal negligible damages.
Lastly, he needs a visual rework, so might as well.
To fix his morphing gameplay, I think that some elements have to go, and some others be more centric to the kit (if the kit was all based around movment speed, the early bombs would most probably not be as strong… they wouldn’t even exist actually)..
To fix his former problem, I only need to design the kit in a way that it leaves more levers for balancing. Right now, the levers are very sparse… You can alter bomb base/scaling damage, and it will hit mid Zilean. You can alter his Rewind amount/cd to hit the very core of his kit (actually, mostly his haste/slow and ult). You cannot use his passive as a lever as its pretty binary with the current value and the actual value of %xp is very hard to measure. You can change some metrics on slow and ult, but all in all it won’t affect him that much… Meaning that there are very few actual modifiable values.
I didn’t touch his Lore, because it’s pretty nice actually. (N.B. I left this one line as-is since I found it coincidentally funny)
#Zilean, the Chronokeeper
##Innate - Rewind
Every X seconds (affected by CDR), Zilean lets out a pulse reducing all nearby allies cooldowns as well as his own by a short amount. (few seconds would be roughly 10, short amount would be roughly 1).
##Q - Decrepify/Rejevunate
Enemy Cast : Deals X/X/X/X/X magic damage to the target over X seconds and adds a stack of aging to the target that lasts up to X seconds. Aging buffs all further Decrepify casts' damage by 25% stacking up to 4 times. (roughly 110-120% of the Cooldown, Cooldown should be roughly 150% of the duration).
Allied cast : Heals X/X/X/X/X health over X seconds to target ally or self and applies a stack of REvival. Revival buffs all further Rejevunate casts by 25% of their base Hleath Regen up to 4 times.
##W - Test of Time
Zilean distort the time around the target, slowing all enemies with X/X/X/X/X units (slightly raising with ranks) by X/X/X/X/X% reducing as the enemies move inside the zone.
##E - Time Warp
After X/X/X/X/X seconds, Zilean warps back to the location of the cast and half of the damage he received during that time is healed back. While warping time, Zilean deals greatly reduced damage (I'd say roughly 50% damage to outweight the heal and make it a very unimpressive 1v1 dueling ability).
##R - Chrono Shift
Zilean places a protective time rune on an allied champion for X seconds.
If the target takes lethal damage during that time, they will be placed in stasis - making them untargetable and invulnerable. After 2 seconds, the target is revived with X/X/X% of its max health (+ AP). (The AP scaling is flat HP, not %HP).