Okay, so I'm back to iOS 4.2.1. While I was on 4.3.3. the two lines removed did help with the animations, but the overall feel of the phone still felt a little weird. I read through the posts to find out if anyone found out what the two lines actually did, because apparently they are there for a reason.
So they launch applications while loading them as well.
BUT...
So this does line that has been removed, and replaced with the new one.
"<key>launch-applications-while-
animating</key>
<true/>"
Found in the N88AP.plist in iOS 4.2.1
So I replaced the two infamous lines in 4.3.3 with these lines, seems to be even smoother now. May just be placebo, but feels just like 4.2 now.