Your question of "why" we want to use POCOs is actually a pretty good one. I think there are two main reasons why we've been using POCOs in the past. One is an OK reason, the other is not a very good one:
1) We want(ed) to keep our business layer vendor agnostic. This is the "OK" reason. However, after doing some soul-searching we aren't sure it's worth the effort to try and keep LLBLGen Pro entities out of the business layer.
2) The less good reason is that we often times just used POCOs as business objects that made it out of the business layer--even if they were less simple than they needed to be.
In other words, I think we are OK without auto-generating POCOs. We'll just manually create simplified business objects when we need them and we'll use the LLBLGen Pro entities everywhere else.