Should the quality of the mic pre in a consumer grade interface be a determining factor when decided which one to buy? Is motu better than digi in this regard? What about others?
Is there an interface out there with high end mic pres?
Let say I'm using a Digi 003, but rent a class A amp for a session. Can I bypass the built in pres?
If your only pres are the ones that come with the interface, and you expect to use them for some period of time, then absolutely the quality of the pres should be a, but not the only, determining factor. In that circumstance, the pres are probably more important than the conversion. However, there are other factors -- for example, if you really want a protools platform, that are going to limit you to certain brands.
I've not used the Digi 003 (only the 002 and 001) so I don't know if the pres were improved from prior models. The Digi pres I have used were OK (although we immediately replaced them with a Presonus Digimax LT which we thought sounded a bit better, YMMV) and I expect that the MOTU and RME stuff at the same price point is pretty comparable. At that price point, not a lot of the cost of the unit is going into the pres.
It is quite common to use an interface, like the Digi and then use the inserts or line ins for other pres. I have an Aardvark Q10 that gets used that way. The pres are OK, but I now have lots of other pres that are better, so I simply use the inserts and bypass the Aardvark pres. The Aardvark is now being replaced (anyone who wants to purchase used Q10 let me know), but I'm moving to separate pres and converters (largely because I have separate nice pres), rather than to another bundled product.
Ultimately you need to look at the entire feature set, both in terms of what you need currently and how you expect your recording needs to develop in the future. For example, if I expected that I was going to purchase outboard pres in the near future, the pres that come with the interface take on less importance and the conversion and software platform become more important. If you really want protools, that will limit your options as well -- I use Sonar currently so protools (and thus Digi) isn't important to me.
Personally, if I was looking for a bundled interface at the moment, I'd look closely at the RME products like the Fireface. From all appearances and testimonials, they seem to be well engineered products that pretty much perform as advertised.