There comes a point in car audio when you cannot move forward and some things become essential or inevitable. To have more control over your system you need to introduce a new friend, and that is a digital signal processor.
Phase, its very important when it comes to audio. I have played a lot with it, first you won't even recognize what phase shifts are doing to your system, then when you start feeling it, it would sound as if its killing the dynamics, for me it was hit and trial in the early stages of tuning, then I started to hear it. Since you're dealing with a 2-way setup you only need to work between your midbass and sub, for now you can try different things like I did once. Bring back your sub the same phase as your midbass, and then change polarity of one of the drivers after the crossover's, first try drivers side, and listen, then try passengers side and listen. I would suggest the passenger's side. An out of phase sub would sound as if its placed in the dash board, try that too. This is all you can do right now. Since I was playing with MS-8, I did not have much controls on the phase, and I had to manually introduce them and re-tune and listen, and my DSP was doing all the magic.
As Shahid bhai stated, reflections, install, and placement are the factors that would always influence your acoustics one thing is for sure, keep experimenting, there would be a time when you would start liking what you hear, but not for a long time.. 
