I think this is a really good suggestion - certainly a topic that is becoming more and more relevant. We tried to touch on this in the text, not to knock BioPerl, but their objects are generally huge (even for simple things) mainly because of the need to ensure that they all mesh well together, and ensuring backwards compatibility, amongst other things. As biohisham says, this interoperability of the whole suite is it's greatest strength, but certainly can be a weakness too.

I have generally taken to rolling my own stripped down objects, and using caching when things get really hairy.

I asked a question on this sort of topic before ( Storable Objects ), and for that problem I did end up setting 'store-points' where I would cache the appropriate info as certain critic points. This worked, but certainly isn't applicable to all cases, especially ones like you mention where the processing isn't so linear.

If you have an example problem (and solutions you tried), please post it here, it would be good to get discussion going - as I said, I think this is a very relevant problem.