I'm assuming network speed/bandwidth has been eliminated since it was a SQL upgrade.

So this may be down to differences in functionality between the 2000 distribution agent and 2008. Maybe execution of the repl procs on the subscriber is slow due to blocking or poor plan.

Did you run sp_updatestats post subscriber upgrade?

Are you able to trace the sp_MSins/upd/del procs to see their execution and test speed?

You could also look in the procedure cache, its possible the 2000 agent has a different plan to 2008.