I just want to point out that any stigma people might have for GameMaker at this point is meaningless. It's a professional development tool, and high quality games are being made with it and getting physical releases on modern consoles. I hope that NESmaker can eventually live up to it's example, and if the games being made and kickstarted with it are any indication, it may just do it. If you've worked hard on your game, and made something exceptional then take pride in it. Have faith in your effort. People using your tools as an excuse to try and devalue it just makes them look jealous.
And for the record, I was also worried in the beginning that it would result in a slew crappy games being sold as overpriced collectables. Thankfully that hasn't been the case at all.