Currently, there doesn't seem to be a way to prevent iTunes from pulling in the voice memos. The closest I've been able to figure would be to have a script or launchd item that simply removes anything that it sees. Preferable copying them to another directory for storage.
Update: October, 2017
I've switched to using Just Press Record which is dedicated to voice memos. It's fast to start and also creates transcripts. They're pretty good most of the time, but sometimes they get pretty far off. It's a nice feature, regardless.
The app costs a few bucks, but it's well worth it. (And, I like to support developers so they can keep working on software I like.)
It sounds like you have a couple of options to try.
Approach one: First, backup your wife's iPhone 3 in iTunes. Then plug your iPhone 4 into iTunes and on the initial screen for your device select Restore. Select her most recent backup. This should put all her settings as well as apps on your phone. After this you can change settings to suit you best
Approach two: Turn on iCloud on your wife's phone, and plug it in and lock it. After it is backed up. Wipe your phone (Settings > General > Reset > Erase All Content and Settings Warning this will completely delete everything off of your phone!!). Then, when you boot it up, click restore from iCloud and sign in to your Apple ID there.
It is important to note that all her settings (including email, etc.) will be synced in either of these methods. You can obviously change that after the restore, but both methods should provide all the apps and such. I'm not familiar with how it would work having two iPhones with the same Apple ID in the long run so there may be other bumps down the road with this process.
Depending on where songs were bought, you may, with her phone plugged in, have to select File > Transfer Purchases from "her name's" iPhone. It will prompt you to login with your Apple ID, and should transfer the music to the computer. From there, you should be able to just copy the music onto your phone. Otherwise select the Music tab with your iPhone 4 plugged in and select the music you would like to sync to your phone.
Best Answer
I have been a developer for little over a year and had have not noticed any slowing down since and because of Xcode - the only thing is that sometimes making backups takes a long time, if you do not backup your iOS device everyday - but I don't see that being related to Xcode.