On slotted minis, just use your side cutters to remove the slot. Then file down the rest. I use miniature rasps to remove most of the slot remainder, then the files to smooth it out.
I also do not like the intergral bases. I am also confused as most of those type bases I have seen will not stand up on their own, having flash or miscast. So I find it strange that a gamer will not take time to glue a mini to a base, but would have enough time to file down the base.
Now having said that, there is a point that you pretty much want the integral base, and that is on the small scale infantry models, say 15mm or smaller. I couldn't see pinning 300 little mens feet to a stand.