seems fine to me. i guess we just need to make sure to wipe cache and dalvik before we install versions above 1.0.
as for the messaging apps...i think any third party messaging app should work with MMS, like go sms, chomp, handcent, etc.
as long as we have the ability to disable any third party ones and just keep regular, it works for me.
I will try to make this clear in the OP but this is how it will be:
If updating to a newer build from current build, such as CyanCoreV1 to V1.1, just flash it. You dont even need to flash gapps.
If going from one rom to another, such as CyanCoreV1 to CyanCore Kexec V1.1, you will only need to wipe data/factory reset. The other wiping (system, cache and dalvik-cache) are already wiped in the updater script. You will need to flash Gapps.
If going from any rom to a V1 version, you can just flash it, because V1 versions auto-wipe data for you. You will need to flash Gapps.
As for the messaging, I will also make it clear that you do not need to use both, in fact I encourage you to uninstall the one you dont use. I have made it so that the stock messaging is uninstallable. I just include them both because people have their preferences. You have a working sms/mms in handcent, but you can uninstall it and use any other.