Do you mean the TRU reissues or the Encore reissues? You say "TRU Encore set."
Please clarify what you mean.
Or I'll just describe both.
TRU: Prime has short smokestacks.
Encore: Prime has the long smokestacks like the original, but the decals are pre-applied, which is more convenient to those who aren't good with stickers.
TRU: Starscream has SUPER LONG missiles.
Encore: Starscream has normal missiles but has a different colored cocpit, which I find rather annoying.
TRU: Soundwave has an expanded cassette door that can fit 2 cassettes. Comes with Ravage and Lazerbeak. Lazerbeak is horribly deformed worse than any KO I've ever seen.
Encore: Soundwave has the original door and only comes with one cassette, but it isn't deformed. Soundwave is a lighter blue. I didn't ask why.
There you go. Hope this helps.