I just got my MotoMaker yesterday, and I was basically in the same boat. I was initially going to just unlock the bootloader, install TWRP, and install SuperUser, but the Moto site was rejecting my device key. I usually will immediately root a device and install Titanium Backup to install my standard set of apps. I gave up waiting for Moto to update their db and started installing apps without unlocking. Most apps I use don't really store much beyond some basic settings locally, so I just re-downloaded everything I wanted from the Play Store and logged into everything again. The few apps that had locally saved data that I wanted to transfer (games, mostly) I ended up using adb on my computer to backup individually, then used adb to push the apps to the new phone. This worked for most things... some apps don't let you back them up. My biggest concern was Google Authenticator, which I use for a number of websites. For that, I had to cheat. Since my existing phone was already rooted, I used adb to pull the stored secrets database off the phone (which you can't do without root). I found this awesome tool which lets you generate QR codes directly from a Google Authenticator db file, and used that to add the secrets to a freshly installed copy of Authenticator.
In the end, the Moto site finally let me get an unlock code, though I think I've decided to skip that, at least for the time being. Unlocking the device wipes it, and I've got things installed and configured the way I want. I don't see myself wanting to push any non-stock roms to this (I really like the Moto additions). I still want root (mostly for backups, though it does make tweaking the device a bit easier), but I can live without it for now.
Device: Moto X