I had hoped that they would be full of interesting experiments with different transaction types or smart contracts or different fee-setting algorithms or maybe some innovative scheme for instant transactions.
These things are very complicated and take a long time to understand, I doubt there are more than a few people in the bitcoin community that really understand them. I'm not even sure these things belong in the block chain instead of being handled outside of it (via Open Transactions or something similar).
Instead, it seems like you've been too busy dealing with low hashrates and transaction-spam attacks, and have been spending all of your time re-inventing a lot of infrastructure (exchanges and block explorers and mining pool software and etc.).
Extending the single-purpose bitcoin infrastructures (exchanges and block explorers and mining pool software and etc.) to be multi-coin is a real accomplishment. Sites like allchains.info, blockexplorer.sytes.net, and the multi-coin exchanges are a big improvement over having lots of coin-specific sites. You might not consider them innovative, but you aren't giving them enough credit.
Most of attacks on the alt-chains were possible against bitcoin too, bitcoin was just lucky that no one attacked when it was young and didn't have the value it has now. Even so, a well-funded adversary could easily spam the bitcoin block chain. Be glad that these issues are being worked out on the alt-chains where the stakes aren't as high.
There has also been a lot of experimentation with the fundamental economic models. No one knows if a coin should be deflationary, inflationary, or stable-value, nor do they know the best way to accomplish the goal. Pre-mining to provide funding for improvements versus no premine and no funding for improvements has been another area of experimentation (it looks like pre-mining lost). The economic basis for a coin can't be changed easily (if at all) so it isn't surprising that is the first area that is worked on.
Merged-mining is pretty innovative, as is namecoin, both were developed this year.
I'm curious to hear what other people think: will altchain innovation pick up in 2012? Am I irrationally biased and just not seeing the awesome power of (insert-your-favorite-altchain-feature-here)?
I think you are trying to get people riled up so that they try and prove you wrong.
I wonder if that means the experimentation will only happen with brand-new blockchains, and if a blockchain will only really take off it the inventor manages to "get it 99% right" the very first time...
Your probably right on this. It is very hard to make substantial changes to an existing block chain.