"Standard" scripts is merely miner bias. It's a flaw that the software developer is allowed to force his biases on miners,
The vendor of the software you're running (the bitcoin development team overall) doesn't believe that the risks (of software bugs, DOS, and bloat attacks) is well enough understood in the software they're releasing to leave that functionality fully open. Especially because use of the corner cases in the chain may make it difficult to fix them. It's a conservative position that some people don't agree with but the people who don't agree aren't stepping up to provide the QA evidence to convince other people of their confidence. ::shrugs::
I'm happy the reference software takes a conservative position, though I also hope this position is a short term one that will go away with more experience and testing.
Eligius already will accept any transaction, "standard" or not, without bias.
Indeed, and Eligius' willingness to do so indirectly cost MTGOX many thousands of bitcoins when a software bug caused them to send some weird transactions that Eligius mined though this is clearly not Eligius' fault as MTGOX compounded their own error by then explicitly directing eligius to mine them.
Can you point to a positive use of Eligius' mining of non-standard transaction yet? When bluematt and I tried using a non-standard transaction for a puzzle a few months back we couldn't manage to get Eligius to mine it. So I have no examples to suggest.

I ... don't mean to argue that you're doing a bad thing there, but I think the case that what you're doing is an important improvement is fairly weak. With only one moderate size pool (and perhaps some tiny solo miners) accepting non-standard txn at least the DOS/bloat exposure is limited by the small number of blocks mined with those rules.