Nicely done video, but the audio comparison of old vs. new is useless of course. I'm glad the video is focused mainly on the install itself (and lacks the display of dancing coins, or vibrating panels and gas caps
I agree with Taibanl that parts of your upgrade path could have been done in a more OEM friendly fashion, especially the amp rack, the head unit and the tweeter locations.
From a sound quality perspective, I'm sure the Pioneer will give you better SQ and more flexibility than the OEM HU. It would help if you showed how many channels of amplifications you have, and how they are controlled by the Pioneer. I hope you decided to bi-amp the MB Quart set, as separate time alignment on the woofers is extremely beneficial. The subwoofer in the trunk floor compartment I have to say is probably not the best choice. That's the only part of the system where the OEM look has to be "sacrificed" in order to achieve the best results. A fiberglass corner enclosure, for example, will sound better, and be more efficient (louder).
In the end though you have to like it and if you're happy with the way it sounds then I'm sure it was worth it. If you're one of those people who constantly strive for improvement, then I'd suggest you meet with some local forum members and listen to their cars and see if you like some of their choices better or not.