The worst problem with Lua is that arrays start at 1. That is way too bad for me to use it. I only use it to configure Awesome WM, but it sucks for everything else IMO because of "tables" starting at 1.
I've done a lot of work in Lua and haven't really found it to be an issue. As long as you stick to doing things the "lua way" (i.e. pairs / ipairs), the specific indexes matter very little. Every once in a while I'll have an, "oh yah," moment where I use the wrong index and something doesn't work, but I don't see how it's a deal breaker for anyone.
There are many features of Lua that have caused me more problems (the somewhat inconsistent string conversion, for instance).
It is a minor mind shift. The kind I find alternately annoying, or a fun challenge, unpredicatbly.
When I was doing Lua stuff I ended up writing some FP-style helpers and other functions for iteration. This cut down on the number of times I had to think about the table indexes (and was helpful in general).
It's annoying, especially if you switch between languages frequently.
My first task in Lua was to build a solid collections library (modeled after Ruby's), so this issue comes up far more infrequently for me now. (e.g. I use :first(), :last(), :push(), etc instead of [1], [#length], [#length + 1])
