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For the re-installation, I'm looking a smooth, straight line between
baseboard and wall, but I would like to avoid the problems mentioned
above (dirty, difficult to remove baseboards after the fact). Any
suggestions on how to achieve this? What type of filler/material
should I use as interface between wall/baseboard? Lightweight
spackling? Some special type of caulk?

What about method of application? What's the best way to get a smooth,
straight line?

Filler? Caulking? What kind of crappy job did you have or crappy walls?
If the walls are reasonably straight all you have to do is nail the
baseboards in place.