Ok, you I guess the first question really to be asked is what are you wanting out of your system. If you are wanting some really good speakers, but are only powering them with a 4x40W then stick with coaxial speakers. If you want something and are spending the money on a really good install and good speakers then you need to get a good amp to power them. Figure out which speakers you want then find and amp that will pair well. It doesn't matter if you spend 700 or 5000 on speakers, with 40 watts they won't sound nearly as good as they good.
As far as subs go, I would do something better than MTX. Maybe some JBL or Focal or ARC subs.
You have to think of a system like water running through a pipe. If you are running 8" pipe but have a 1" section then it doesn't matter how much 8" pipe you have the 1" is going to control the flow.
Now, before the comments get made, do not take this sexually please.