I loved playing this game the first time through (imported it in July 2008), but the scoring system is preventing me from building up any desire to go back to it since everyone figured out the way to high scores is scout rushing the flag. Do you think they should change the scoring system for the sequel?

no

well there is a map that you can win with a S rank in one turn. 
Then you can do it over and over again to cheat out experience points

No. But a smoother cutscene transmition would be tits.

" @trophyhunter: one ofthe first ones where you have to cross a tiny bridge at the end? "

I just started playing the game, for the first time, and I do find the scoring system is a little annoying.  My problem is I like to take my time and make sure I've killed everyone but when I do that I end up with a medium rank.  The more I play the harder the story missions are getting so I think I'll be forced to replay the Skirmish levels and use the scout to win or I might end up underpowered and find myself getting stuck. 
 
Still, my biggest problem with the game is being brought back to the menu after every cut scene when some of them are barely a few lines of dialogue.  That and the lack of Trophies.