1. The ability bonuses are different. Only slightly, but it would have been easy to make them the same. Strength and Dexterity don't apply to combat rolls.
2. The skill list is the same as Tri-Stat, and completely different to d20. Other d20 games add or remove a few skills, but SAS changes them completely, ignoring some important skills.
3. The combat rules are significantly different (random ACs, defense rolls, random Strength bonuses, rerolling initiative).
Ok, in order:
1(A) - Different bonuses: Very easy as a GM - pick the one that best suits your game and use it.
1(B) - Strength and Dexterity not applying to combat rolls: That was done for a very obvious reason - since armour was changed to damage reduction, the change had to be made to Strength. Currently, in D&D, the Strength bonus to hit (which should more accurately be called "to harm") represents a person's ability to power through armour and damage the target. By changing armour to damage reduction (which we think it a better system), we had to pull that from the to hit roll because armour was no longer a factor in AC. It would be foolish to have the Strength bonus apply to a character's ability to hit _and_ ability to inflict damage. Strength would suddenly be twice as effective. Pulling the bonus from Dex was largely a game balance issue. ACs had dropped, the bonus was pulled from Str, there are other skills and abilities that provide the appropriate bonuses, etc.
If you use an SAS character in D&D or vice versa, you just use the appropriate base system. Pulling Sentinel into D&D for a spandex fantasy game? Now, he gains a bonus to hit due to his high Strength. Why? D&D adds armour to a character's armour class so it makes sense. Pulling a red dragon into SAS for a night of fiery mayhem? Pull the bonus because armour is now damage reduction. Very simple.
2 - If a skill list is a problem, then you are really stuck thinking inside the box. The change was obviously done for compatibility with Tri-Stat but it does not negate compatibility with regular d20. What is a skill? It is a bonus to situational rolls. When you are doing something that is covered by your skill, you gain a bonus. Thus, when you pull a D&D character into SAS, don't bother changing their skill list. Keep it the same. When they do something covered under one of their skills, they gain the applicable bonus. Same thing when pulling an SAS character into D&D. For this, there's _no_ change that is required, imho.
Alternatively, just change the skill list. Really, keep the combat skills (since they are required for game balance) and the Power Usage Skill (since it's needed for powers) but otherwise, if you want the D&D skill list, use it. It doesn't break the game. Same thing vice versa.
3(A) - Random ACs/Defense Rolls - See the DMG. We didn't add that - WotC did.
3(B) - Random Strength Bonus - What is the point of rolling 1d6 when a person has a +45 damage bonus? We wanted there to be some variation in damage inflicted when superstrong characters get into slugfests. If you want to ignore that, go for it. It isn't vital to the game - it was added because we feel it makes a better superhero game.
3(C) - Rerolling Initiative - Reread the initiative rules. We suggested rerolling because that's how we think it should be done but we also very clearly state that alternatively, GMs may want to just roll once. If you don't want to reroll - just roll once.
3(D) - Different Rules in General - We made additions to the rules to encompass the superhero genre. There were exceptionally few _changes._ If you look closer, you'll notive that virtually everything is the same or has an obvious reason for the change (make a better superhero game). We made additions (knockback for example) because they were needed and d20 didn't have something already in place. We also "ignored" some rules like attacks of opportunity because 1) we didn't think they were in genre and 2) when you're dealing with characters that can run or fly from one side of the city to the other in one combat round, attacks of opportunity suddenly become pointless.
In general, I think you might want to take a closer look at SAS d20. It is far more compatible than you seem to believe.
