Converting/distilling some of my comments into an answer...
Yes, we should update our tag wikis to not unconditionally point people at webapps.SE when they have an AWS or EC2 related question.
But where do we send them instead? Actually, the answer to that question becomes more like a long
switch statement (in a language such as C or Java), where the condition for each case is quite complex (and, indeed, overlapping; have fun with that!)
At the risk of oversimplifying, we have the following technology sites that are potentially relevant to users of EC2 / AWS in general:
- Super User: A fairly decent "catch-all" for help using applications (they don't necessarily have to be GUI applications; we cover all sorts of console apps, bootloaders, etc.), as well as the de facto "Windows.SE" (for lack of an actual windows.stackexchange.com). So, if you run Windows in the cloud (on EC2, Azure or anywhere else), and you have a problem with, say, Windows Update, a registry setting, or your Active Directory domain, you can of course ask those questions on Super User.
- Server Fault: A lot of questions specifically pertaining to sysadmin tasks that are completely outside the domain of "regular users" are certainly on-topic on Server Fault, and in many cases the fact that your system is an EC2 instance on Amazon doesn't matter. Whether you're trying to add high availability to a Jenkins cluster or expose a block device over the network using iSCSI, many tasks that EC2 users might need to perform (or AWS users in general) could be covered by Server Fault. This is also the site where you'd probably want to ask most questions pertaining to the AWS services themselves, like Elastic Beanstalk, RDS, S3, Glacier, etc. although a fair number of questions along those lines would get answered on Super User as well.
- Ask Ubuntu: Obviously, if you run Ubuntu on an EC2 instance, any questions pertaining to software on Ubuntu (especially the main packages, but also any peculiarities about how Ubuntu works vs. other distros when trying to run third-party software) would be on-topic.
- Unix.SE: If you're using some flavor of Linux or another UNIX like SmartOS, Solaris or a BSD, and you just happen to be hosted on EC2, and run into some question about an application or configuration setting, it's perfectly fine to ask it on Unix.SE (even if it's about Ubuntu!)
- Stack Overflow: If you're writing code to interface with Amazon's APIs to automate tasks involving AWS (for example, code to send email with the Simple Email Service (SES)), you'd want to get programming help from Stack Overflow, and this would be on-topic there significantly more than the other sites listed thus far. Super User might tolerate it too.
- Web Apps.SE: Really the only scenario where you might pose a topical question about AWS on Web Apps.SE would be if you have a question about using the (admittedly somewhat complicated) AWS Management Console. This is very much an "end-user" application, in that, the workflow involves putting in your login/password, then clicking through a bunch of links and buttons, entering data, etc. The format of these questions would be no different than a question about gmail's interface.
The problem is that users are generally not clueful enough to really understand where their question belongs. The user is working on a problem that is related to something they're trying to do with a complicated stack of software, usually something crazy like Hazelcast with jHipster on Tomcat on Ubuntu on EC2.
When they think about all the technologies involved, it's fairly likely that they will randomly pick one of the technologies in the stack and try to "blame" that, or just blame the thing they're most unfamiliar with (the "gut feeling" approach). From there, they'll attempt to discern which site on SE is topical for that "thing". If they then decide to blame EC2 for their Hazelcast configuration problem, they'll try and ask it on a site that seems like it might accept EC2 questions.
We can certainly update the tag wiki, but our tag wikis get so few views to begin with that I doubt very many people will benefit from it. The underlying problem is going to remain for a long time.
Sadly, I don't think you'll stop getting off-topic EC2/AWS questions on Web Apps (yes, even ones migrated there from Super User by 10k users who don't understand the question) any time soon, even with a comprehensive tag wiki update.
The problem of knowing what information is relevant to the question and what information is orthogonal is extremely hard, and only a small subset of users are good at slicing and dicing things that way. (Problems that cross-cut the entire stack are relatively rare, in my experience, but they do occasionally happen.) Unfortunately, AWS adds another technological layer of complexity to an already complicated field of software dependencies used by many applications, so this problem is only going to get worse over time as other services start to layer themselves on top of existing AWS services.
It's not going to get any easier to classify these things.