Right now on Live, most mushrooms are worthless ingredients because they contain "Ravage" traits that are useless for potion-making. They're good for leveling alchemy, but not much else.
I had hoped that poison-making would bring these ingredients to the forefront, but I've been disappointed by what I've seen on the PTS.
Example 1: stamina poisons
Made with Ravage Stamina mushrooms:

Made with Restore Stamina flowers:

I can understand your reasoning behind this: the Ravage poison has a longer negative effect duration, and the Restore poison has a shorter negative effect duration, but a positive (to the user) effect added on.
But in practice, it just means that the Ravage poison made with mushrooms will be virtually useless, and only the Restore poison made with flowers will be useful.
Why? Well, in PvE, there is absolutely zero benefit of increasing the ability costs of monsters and NPCs.
In PvP, while the longer cost duration might seem useful at first glance, it is useful only if your opponent is a stamina user. Since you cannot change poisons mid-combat (unless you slot different poisons on different bars, but that is problematic on its own), the mushroom Damage poisons are therefore less versatile than the flower Drain ones: If a Drain poison doesn't affect your opponent's main resource pool, at least it would restore your own main resource pool. And in even if fighting an stamina-based opponent, losing a little bit of duration on the cost increase is well worth the amount of resources that you get back.
Oh, and even in PvP areas, you will still fight PvE enemies: e.g., Daedra in IC/sewers or guards at keeps and resources.
So while the two types are a bit more balanced in PvP, it would seem that the flower version is still better overall.
Example 2: spell power poisons
Made with negative traits:

Made with positive traits:

Again, we have a similar imbalance. Even in PvP, I don't think a few extra seconds on Minor Cowardice is really worth the loss of that spell damage buff.
Why is this a problem?
It's problematic because ingredients with Ravage traits are already far less desirable than ingredients with Restore traits, and certain flowers can sell for 10x more than mushrooms on the guild markets.
While I can understand the thematic angle that ZOS is going for--with longer negative effect durations on the mushroom poisons--in actual practice, the best poisons are, unintuitively, made from flowers with positive Restore traits rather than mushrooms with Ravage traits.
This will lead to even greater demand for flowers in the player economy instead of fostering more balanced demand between the different ingredient types. If you think flowers are currently overpriced relative to mushrooms, just wait till the new poison system comes in: it'll get even worse.
Possible solutions
One easy solution would be to reverse the effects. For example, poisons created with Restore Stamina flowers will result in Damage Stamina poisons and poisons created with Ravage Stamina mushrooms will result in Drain Stamina poisons. This would make mushrooms the most desirable ingredient for poisons, and flowers the most desirable ingredient for potions.
Alternatively, some adjustment of the effects might help make the choice between the two more meaningful. In particular, it seems counter-intuitive that poisons made with positive-effect ingredients would even be considered poisons in the first place--if potions made from negative-effect mushrooms are utterly useless (they're self-inflicted poisons), why are poisons made from positive-effect flowers so useful? (And arguably, too useful?). A reduction of the durations/potencies of the positive-effect poisons and/or adding a restorative effect to the negative-effect poisons would bring the balance a little bit closer.