Half-baked 1:why the heck do we have 8 decimal places for the transaction amount?
That's just a design decision that had to be made in an early stage, when it wasn't clear yet what the potential of Bitcoin would be. I think it was a good decision at the time, since the number of bits for storing values is still small compared to e.g. scriptsigs. As other posters have mentioned, it can still be useful in the future, even when we will never have really small (satoshi-sized) transactions in the block chain.
Half-baked 2:Here's an idea: Reject blocks larger than 1 megabyte that do not include a total reward (subsidy+fees) of at least 50 BTC per megabyte.
How is that arbitrary limit better than a "number of transactions" limit?
Also, you choose quite a high number: it would be about 0.01BTC/transaction. How is that going to allow "satoshi-sized" transactions?
About coupling the transaction limit to difficulty:Interesting idea. For now I only see one problem: it is possible (and likely) that in the future processing power will increase at a different rate than network+storage, so you could still run into trouble. But since it's a "better approximation" of the optimal transaction limit than a constant limit, you'll probably run into trouble "less often".
Just make sure it's set low enough so that people can run full nodes at moderately small investments (maybe not for the average consumer, but at least for a non-profit hobbyist).