I know Scrum so I'm writing from that perspective.

I'm not sure about "agile." In my experience, "agile" means "we have no workflow and it's a fucking madhouse."

   > In most scrum processes 3 weeks of effort would 
   > not be accepted, and the story would be "broken down"
   > into smaller issues such as "implement an upload 
   > button".

Yeah absolutely. But what's wrong with that?

At some point, this will need to happen.

One of the primary values of Scrum is that it forces you to break a story down into discrete tasks and estimate them as a team before the work begins.

This is a great chance to pool your knowledge as a team. Suppose a team consists of developers A, B, C, D, and E.

Well, implementing the Excel imports might involve 3 smaller stories. The first story might involve concerns that A and E have, and maybe there's actually a really easy way to do it that C knows about because she's done it before, and D's done it before too and knows about some pitfalls. That's a friggin great conversation to have.

Now, you don't need Scrum to have that conversation, but Scrum's cool because it makes it nearly impossible to avoid it. Now, naturally, you certainly don't need Scrum to have that conversation! A healthy team of high achievers with great communication skills would have it anyway! But, the reality is... that conversation often doesn't happen without some kind of process (Scrum, or whatever) to make sure it happens.

    > Even worse scrum projects emphasize anti-patterns of "parallelizing" efforts

This is really not my experience with Scrum at all and I'm confused as to why you think this harmful sort of "parallelization" (the kind proscribed by "The Mythical Man-Month") is some intrinsic part of agile/Scrum.

Not familiar with Jira, but we used Pivotal Tracker and it lets you specify which stories are blocking other stories.