The '91 Basic Set is better because it has LESS in it than the Advanced Set.
Grubb took his best ideas from his Advanced Set and kept them for Basic. He cut out the rules and details he wrote in an attempt to compete with games like DCH and Champions back in 1986. Basic is easier to learn and play because Grubb streamlined his game for Marvel fans to make roleplaying in the Marvel Universe more accessible and less complicated.
My advice:
1) Use Basic as your foundation.
2) Get Realms of Magic to complement Basic for your mystics and campaigns involving magic.
3) Get the Ultimate Powers Book but:
(A) only use Standard Rank Values when generating ability ranks, just like in Basic and Realms , and
(B) Modify True Invulnerability as Resistance v. the 13 things it is proof against, then along with all of the other Resistance Powers in the UPB apply the rules for Resistances on pages 28 and 29 of Basic.
4) Get Lands of Doom. The devices and machines of Doom, plus the writeups available for any campaign involving Dr. Doom are priceless additions to the game.
5) When you don't like a rule, overrule with your own.
Using Heroclix maps:
On a Heroclix map, areas are 45 feet , not 44 yards.
One square is 15 by 15 feet.
Each 3 X 3 X 3 "block" on the map is an area.
You can use the movement rating on the character base , or figure that for each area that the character can move in MSH, he can move 3 squares on the Heroclix map.
If you do this, then characters with a Remarkable of higher END could move 9 squares, Poor to Excellent move 6 and Feeble moves 3.
Flying characters with Typical Flight would be moving 18 squares (270 feet per turn).