$3000 system sounds bad. Why?

Finally got a new system installed yesterday, but it sounds worse than stock. I can't really explain what is so bad about it, it looks like mid bass is absent, middle-high range is too rough and sharp. Rap sounds more or less ok, but dance and especially rock are just awful. Bass guitair is not reproduced neither by subs nor by component speakers properly.

I feel like front/rear speakers should carry more mid-bass or something, yesterday I spent a few hours playing with deck equalizers and settings and can't do  much about it. Also mid range has some "metallic" tone in it, especially when playing MP3s with increased mid tones in equalizer, is this a crappy deck feature?

Here is the system in Prelude'92:

Deck: Pioneer MP7800

Front: JL XR650 CS

Rear: Some not-so-good 60w infinities

Subs: 2x10" JL W3v3

Amps: Alpine MRD-M1005, Alpine MRV-F345

Can someone please suggest some "universal" crossover settings for such kind of system. For example rock bass guitar - where is it supposed to be , in subs or in speakers?

Also in my mother's nissan with its stock speakers and stock deck I hear much more mid bass from speakers, especially from rear ones. Are those better speakers or how to explain this? I would rather listen to that stock speakers than to this aluminium disaster.

3k it is not for installation but for everything, insluding install. Custom sub box is the only custom work here.

external crossover settings on the front speakers.
internal amp crossover settings.
front door sealing/install quality.

Well, I was probably too frustrated when said that it sounds like crap. It sounds ok, but I don't like it. I already downloaded some sample tones, they all are present so it is not some technical issue, just some settings probably, which I can't find. I already tuned all possible deck's crossovers and equalizers and still can't make it sound as I like.

No it is not a big shop, actually I heard a lot of good feedback about them.

I will probably go there and ask them to turn off (or at least make them as wide as possible) amp crossovers so I can use deck crossovers and at least tune them easily

Also XR speakers have some "adjustable midrange presence" according to the manual with "high mid/normal/low mid" options, I will probably ask them to switch it to low mid as well. 

What about installing better rear coaxials, maybe it will add some mid bass? Their current sound presence is almost not existent.