I don't think they were shooting for a Marine look. It was merely a coincidence. This is supposed to be an AU,a fresh start at many different aspects of a Sonic universe. When you bring old characters into a new part of the franchise, all of the strife having to do with them is carried over. Not to mention it would defeat the whole purpose of having a new world to play around with. I've only read the Archie comics 30-54 that were in an edition of Sonic Legacy so I wouldn't understand what's the big deal with Marine. I do know that Archie had a lot of characters many of them being developed to some extent,but there would be no purpose to Sonic Boom if any other characters other than our main four to appear(an exception being lent to Shadow because of SA 2). As StephenKnux has said before that it is a bit dumb to make a similar character design but like I said before it might be incidental. They just couldn't be bothered to research all the 300+ Archie charcters. Yet again,why would you?? Personally,I think the comic would have been fine stopping around the 50s since it followed the fate of Sonic SATAM. I think the SB team is going to add some of the past characters(Chaotix,Cream/Cheese...etc) later on in a theoretical season 2. I thought it wasn't Marine from the start and I couldn't really think of any justification for her being here.
In summation,Sega has opened a new nutless candy bar and they are NOT adding the old nuts to the new bar. It's a(mostly) whole new thing with new ingredients and it's better for the Sonic fanbase to just accept it.