I was in the same boat as you. After receiving advice from some helpful folks here, I went with the 2.1. Although there was a "bad batch" a while back due to a different type of memory chip or something, that issue has been sorted out and the latest version of AKAIO (and if I remember correctly, the official firmware as well if you want to use it) works perfectly fine on it.
As far as build quality goes, according to Another World, who seems quite knowledgeable on the subject, 2.1s tend to be more reliable than their DSi-designed brethren. Not to mention the fact that the former are slightly cheaper. Hopefully he'll post in this thread and shed some more light on the subject, as I can't remember all the details.
My opinion? Go for the 2.1, dude. I totally get where you're coming from, and as a DS Lite owner, you'll get no benefit out of owning a 2i. All software compatibility is the same; the only difference is that the 2i is designed to be able to run on a DSi.