An animated 512 or 1024 sprite is huge and the 1024 especially is going to use a ton of VRAM - probably about 80MB. Large images (512 and up) are a huge bottleneck when compiling, though they are cached and don't need to be recompiled until you change them or reload the project.
I got around it by loading large images at runtime, but I'm not sure how well that will work for animations concerning hotspots, etc.
As far as I know, larger textures aren't a problem for GPUs to render (as long as they support them - stick to 1024 and under), though it will take longer to transfer all those textures to the GPU at the start of the frame. That's generally not an issue, though. The bigger concern is a GPU not having enough VRAM - then it will have to swap textures every frame. Your main problems are compile time and VRAM use.
If you're aiming for 256MB cards (which doesn't mean you have 256mb to work with - the OS uses some, etc.) it might be okay depending on amount of other stuff in the scene, and you could leave the trees animations out and put them back in as the last step before exporting to an exe.
You sure you can't use that animation system in real time on only the onscreen trees? It would be smoother, use less VRAM, load faster and could be dynamic as well. Unless it requires a ton of cpu time, obviously.
It's frustrating having to wait upwards of 60 seconds with a 'Construct is not responding' message every time I want to test my layout.
I hear that. Mine does too.