I am in favor for 2d at most times and that just not for games but in general as visualisation.
With 2d you usually have:
- better overview: important for structured and herichal data, think of a platformer with different jump platforms, or a OS with lots of structural table data.
- simpliefied, ease to read: we are used reading magazines and other print media therefore our eyes are specialized in recognizing characters and illustrations on 2d surfaces. I think the same applies for example on web design- in usually 2d works best
- fast to execute: not just does the design task but also the programming job take less effort and complexity. And because of that there is so much more space for exploring different aspects besides the state of the art of the visuals. For example physiscs, particles, typographics,...ec.t are more to explore.


with 3d you can do well:
- fsuck the player in the game world,- it feels more natural looking not from a abstract perspective like topdown, pixel- iso, side scroller, ect. I think it helps alot transporting the atmposphere way more in some cases.
- exploring mechanics Because in 3d projection you usually see only a limited portion moving the camera is a usual task. Imo. thuis mechanic works best for puzzle, adventure and alike games where you need to find items ect. Seeing objects from different angles can help understanding complex objects better.

hmm well I am certain there are more pro´s working with 3d but usually personally I am more interested in that topic from a design and technical view- not gameplay wise.

so from that a few thoughs on:
technical side
Most flash games or movies are utterly crap from a technical perspective. Some stuff I see on the net and sometimes here on the forum resembles powerpoint presentations alot and I think that says it all.
So seeing once here and there some technical impressive demos (be it 3d, physiscs, particles, ik/FK, sound, emulation,...) is something I really enjoy - partly because with such a big contrast it gives hope and speculation on who the perhaps better future of flash might be.

design side
I like working with 3dsmax alot- its like playing with clay and optimizing every view of the model.
The reuseablilty is very high- not just can you reuse objects mutliple times but also can you display it from different angles. In other words: you give multiple impressions by having to create it just once. I did not wanted to post this before but here is something I am working on recently

Its a 3d test tile set (recycling LTTP tiles) for a new engine,- trying to find out myself what the benefits are instead of the 2d- and how I can share some of the designs. What´s the best way of navigation and when to show what and how.

in the end the 3d chapter in Flash just started and its main attention its gets is because its fresh in the flash world on stands someway out of the crowd.