Compare the pair...
Colours:
25th Anniv. has bright (IMO garish) colours.
Encore has G1-accurate colours (more or less).
Winner: ENCORE
Smokestacks:
25th Anniv. has shortened smokestacks, as do all Hasbro reissues due to child safety laws
Encore has full sized smokestacks due to Japanese reissues NOT being aimed a children!
Winner: ENCORE
Missiles (Combat Deck):
25th Anniv. has ridiculously oversized missiles - even though Hasbro has proven that another alternative is to remove the launching mechanism
Encore has original sized missiles and powerful launching mechanism
Winner: ENCORE
Bonus Goodies:
25th Anniv. comes with comic book (US version comes with DVD), neither of which are exclusive to the toy. It has a sound box.
Encore comes with tech spec card.
Winner: 25TH ANNIV.
Standard RRP:
25th Anniv. RRP is approx. $100 (TRU are selling them for about $80 claiming that it's 20% discounted according to their catalogue)
Encore retails for 5250JPY (Source) which is like $53 for Japanese people.
Winner: ENCORE
(not incl. external factors like exchange, shipping etc.)
...and from what I've heard the 25th anniv. has QC problems which the Encore doesn't.
Overall I'd say the Encore is the better toy between the two. JMO folks. :)