I'm a recent convert to Remember the Milk[0], can't recommend it enough (the apparent stable business model is a plus as well, I recall using them back in the Blackberry era)
I'm led to believe the issues with Clojure (and other JVM languages) on Android are due to Dalvik not being as friendly to other languages as the Sun JVM. I don't blame Google, but it's unfortunate.
The same reasons [0] are why I have a Chromebook. CrOS is limited, sure, but the limits make the thing bloody near invincible (and amazingly productive).
[0] Hangouts are luckily the VoIP of choice for most I work with
APK size takes a small hit, and there's extra work to bring in Java libraries. That's all I've found. I've actually been using their guides when working on ordinary Java-based Android code; their docs are well-written and their SDK maps nearly 1:1 to Google's (helps here that Java and C# are fairly similar to a degree).
Think how exactly the alerts happen is up to the OEM, beyond 'loud noise'. The iPhone uses something similar to the EBS tone in 1s bursts (it was 1AM when mine fired, so I can't say with certainty if it was the same tone or not). I've heard similar from other Android users, but I've shut off the alerts on all my phones since.
Taking it out of USD and changing the units around (even though it's just dropping a decimal point) mentally disassociates 'Amazon Coins' from USD. Microsoft goes even further on the Xbox, 1 USD (+ local sales tax) buys 80 MSP; so it takes a moment to realize an 800 MSP game is actually $10.
Dark Ages would imply that progress was set back significantly by some catastrophic event (ie: the fall of Netscape). Renaissance would be a more apt term, given the rapid advances we're going through.
Most of these are bound to a language: choose a language first (and my answer to that question is "whichever one you're happiest working in and can get the job done"), then figure out which backend to use. You can fret over the framework more after you've already built something that works.
[0] http://rememberthemilk.com