Disclaimer: Stack Exchange employee, so grain of salt and all that.

I'll address your thoughts in order. A lot of this is theory sort of stuff.

- Badge/Reputation fragmentation is not only by-design, it's essential. It's non-obvious, but I've found little demotivates contributors quite like observing someone else being rewarded for the "wrong thing". Setting what's on-topic for a Stack Exchange is always a Big Deal™ to a site's community, for good reason.

We do grant a cross-site association bonus to kick people familiar with the Stack Exchange system over the "new user" line on new sites (http://blog.stackoverflow.com/2010/05/new-automatic-account-... , though the mechanism been refined a bit since that was written). This gets rid of the "having to earn your stripes" pain of moving to your second Stack Exchange.

The user divide is to a degree a historical accident (the multiple cookies at least, which we've alleviated a bit with auto login [http://blog.stackoverflow.com/2010/09/global-network-auto-lo...), but the act of saying "I am interested in this site" is also by-design. People don't like getting signed up for things they didn't ask for, and getting listed on (say) a Science Fiction (http://scifi.stackexchange.com/users) site that didn't even exist when they registered would be sort of evil. I don't think Reddit even has a user list page, so it's less of a concern there.

- I don't think the Reddit/Stack Exchange parallel really works in this argument. There are two big differences that I think matter in particular.

1. The unit of work is wildly different.

Subreddit's can survive on link submissions alone, which is pretty effortless. Comments and voting are gravy, certainly useful gravy, but not absolutely essential.

A Stack Exchange needs both question askers and answer posters in pretty non-trivial quantities on day one. Askers will get frustrated and leave if they aren't getting answers, and answerers will get bored and leave if there's nothing for them to do. Both units of work are also pretty large compared to link sharing. This is why the Area 51 process has a commitment phase, to help get enough of both types of users into the beta on day one.

2. Subreddits are basically aggregating content (link sharing and all), Stack Exchanges are creating it. Both are useful functions, but the failure cases are pretty different. A failed Subreddit has some links that go to maybe boring, maybe useless, but already existing content. A failed Stack Exchange has enough questions to give users some hope, but not enough answers to actually help them.

Basically, a dead Stack Exchange is much more likely to ensnare people and waste their time than a dead Subreddit which makes leaving them up sort of evil. This is a major reason for high-bars for site creation, and killing the failures that still slip through (http://blog.stackoverflow.com/2010/09/pruning-season/).

All that being said, we are constantly looking at the Area 51 process and keep making refinements. It's nowhere near a perfect, or even complete system yet. I'd be shocked if there weren't major changes in the future.

- This feature actually exists, it's just very much for power-users

http://stackexchange.com/filters/new - find questions across the Stack Exchange network based on site and tag combinations.

http://stackexchange.com/filters/favorite-tags - your favorited tags across all your accounts on the Stack Exchange network.

What we've found is that most people are active on a single site, typically their hobby or profession. Something they're passionate about, anyway. It's much rarer for people to be heavily active in more than one (non-meta/governmental) Stack Exchange. While we do build tools for those folks (like the above), I suspect that one or maybe two Stack Exchange per person is the natural state of things. The unit of work is again really different (and larger) when compared to Reddit, which is probably the root cause of such behavior.

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So... I guess the TL;DR is that while there are some Reddit parallels in Stack Exchange, I really don't think most of these hold up. Mostly because Q&A is pretty different from link sharing.