I have been using Blender 2.4 with Unity and that combo is awesome. Blender 2.5 is coming out soon and it looks like it will have a new animation system. I am worried that my Unity projects won’t deal with the new Blender animation system. Anyone know if there will be a Unity update to coincide with Blender?
don’t see a problem there. Unity only supports one specific type of animation, blender already by now has stuff that you can not use.
Unity is bone based animation with keyframes
neither are IK restrictions nor morph targets supported … so nothing should change actually
Unity doesn’t work with Blender files at all; it only makes Blender output to .fbx. So unless they change the .fbx exporter significantly in Blender, there will be no differences.
–Eric
From how I understand it Ton said that despite a complete rewrite of all the underlying code the old files will be completely compatible as this is one of the premises of Blender. I don’t know how much this will affect the FBX exporter but I wouldn’t expect it to make Blender unusable.
Besides ‘soon’ is a relative term. It’s a little more than halfway done so far. It still is quite some time to go, I guess. The GUI improvements haven’t even started yet - only concepts and such …
If it really won’t work immediately stick to 2.48a until 2.5 will be supported again 
As Eric said, Unity imports Blender files by launching the .FBX export script in Blender and then importing the .FBX into Unity. This is done in the background so you don’t even know it’s happening. So the only thing that could cause problems when Blender 2.5 is released is if the Python API is changed in a way that interferes with the export script. Campbell Barton (Cambo on the BlenderArtists forums) is the creator of the script and would be the person to ask if issues came up.
One limitation of the script that I wish Cambo would fix is that it currently only supports bone-based animations. I wish he added object-based animations, ie. object movements and rotations. The only way to do this currently, if you are a Blender user, is in Unity’s native animation timeline…
Campbell Barton (Cambo on the BlenderArtists forums)
I’d throw him a quick “Please make sure this works correctly when the time comes” message, just so it goes on a to-do list somewhere.
Also, “Soon” is no earlier than the end of June according to the recent (very interesting) update on progress:
http://www.blender.org/development/current-projects/blender-25-project/
If I were a betting man, I’d bet just before 2010.