.mov and avi are most likely your best bet to work with anyway, simply because you want to work with uncompressed video when adding effects or any color correction and grading. You should be editing your video in your NLE because it should be able to import other formats as well so it makes sense that the lab products only use .mov and avi
I downloaded a trial version of After Effects a loooong time ago and let me tell you... it has a long learning curve... it does for me at least. I just couldn't wrap my head around it and gave it up with a quickness. I'm just not smart enough I suppose. Either that or it's the fact that I like my UIs' to be streamlined and easy to use. To me AE seems very cumbersome and technical compared to Visionlab where I know where everything is and what it does or what it's capable of doing.
It's like comparing Photoshop with Gimp. To do the simplest thing, you almost always have to go through a needlessly long process in Photoshop but you can do the same thing in Gimp with a single click of your mouse or pen and tablet. I dunno, my thinking is, the less steps that I have to do... the faster I can get my work done. I'm not tossing quality out mind you. It's just that I have a thing for not wanting to waste time on a long tedious process on one program when I can complete something easily on another program. Don't get me wrong... I've seen some awesome and amazing work from AE users and those guys are brilliant by the way... it's just that I think they could shorten their workload when I see them go through so many steps to achieve an effect.
So yeah... VL is the way to go. It is for me at least. You should use whatever is most comfortable for you though. I also wouldn't mind an update of new or tweaked existing features in my all time favorite software. I suggested this a long time ago but it would be cool if we could add our own textures to the optics engine much like we can in the particle and muzzle flash engins... that would really be prime.
I've got another one for you guys... what if you could affect the width of a trunk in the lightning engine anywhere between the start and end point with a slider? Yes no maybe?