They are pretty even in my opinion. SO picking the better set is not an easy thing to do... but I personally prefer Evolution 3.
These matches off Evolution 3 are all must see:
12/14/02 - GSCW - Super Dragon vs Bobby Quance (2002 MOTY)
3/29/03 - GSCW - Super Dragon & B-Boy vs Bobby Quance & Jardi Frantz (2003 MOTY)
8/16/03 - APW LA - Super Dragon & Excalibur vs Joey Ryan & Scott Lost
8/30/03 - PWG - Super Dragon vs Joey Ryan
10/04/03 - PWG - Super Dragon & B-Boy vs The Briscoe Brothers
11/15/03 - PWG - Super Dragon vs Joey Ryan - Guerrilla Warfare match
15. 11/29/03 - Revolution Pro - Super Dragon vs TARO "Mask vs Mask"
10/11/03 - RevPro: "Pride of the Mask" - Super Dragon, Zokre, & Rising Son vs Quicksilver, Phoenix Star, & TARO
Plus you get other fun stuff like his debut match, his PPV match from Japan, and his series of matches with Joey Ryan, TARO and Mr. Excitement. Also his only singles match to date with Scott Lost. PLUS not one but TWO Charles Mercury matches.
Evolution 4 is also a fantastic set, with some really fun matches from CZW (including the amazing 4-way with Excalibur, Quance and B-Boy) Great RevPro matches with Bosh and Slymm, The insane match with Jack Evans from WAR. A floor cam version of the 2004 MOTY Iron Man match with Joey Ryan. Not to mention more good stuff from IWA:MS, England and Germany.. Plus funny Easter Eggs!
Both are must own sets for fans, but personally speaking, I prefer Evolution 3 by a very slim margin.