Placing things on timers make them quite unbalanced. Apep's recent change made him extremely stronger than he was before, especially in 2v2. His design was, as were many masters', based on mana which is the fundamental unit of the game upon which everything is balanced.
Mana generation is slower in 2v2, making timers far more powerful.
Compared to a cheap/medium cycle of 1-2-2-2-2-3-4 previously, the new timer is in 2v2 about 60% stronger for perk 1 and 36% stronger for perk 3. For 1v1, this 16-cost cycle means his perk 1 is still stronger by about 40%, and his perk 3 is the same.
Even with the cheapest possible 11-mana deck (which was really bad), his perk 1 is currently way stronger than before.
Make his perk the following, to balance it for any deck type and any game mode:
For every 20 mana spent, add a random free 2-cost/4-cost card to the top of your deck
Can be more or less than 20, now you can balance it around mana, the real unit in this game, rather than through indirect things like cycle or time
*EDIT: Different idea from Destian, for 20 mana gained over time after having played your free card, add a card. Now there is no way to exploit it, this works exactly like a timer, but is based on mana as its unit and not on time.
For every 20 mana gained, add a random free 2-cost/4-cost card to the top of your deck
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Problems in different approaches
(1) Cycle based: forces down a cheap decktype
(2) Timer based: unbalanced 1v1 versus 2v2, unbalanced strength throughout a match, early/mid/late game have different dynamics, currently far too strong
(3) Mana based: allows bursts of cards to be played

