Agreed! There are lots of places where this tool could be improved! (Disclaimer: I work with people at 18F, Dept. Of Ed, USDS who built this tool, but I wasn't involved and don't have any privileged information and so here are some of my personal thoughts)
If I can add a bit of color:
1. This was developed open-source on GitHub. That means you're welcome to file an issue or comment at https://github.com/18F/college-choice/issues (Given the interest and number of issues filed so far, I'll probably take this opportunity to say that it might be a while before the team gets back to you and appreciate your help and patience!). This shouldn't impress you, but it is, because it's a complete paradigm shift from how government typically works.
2. Average salary is not a great metric and unfortunately, as far as I can tell, the data isn't sliced by major. You're right in your analysis of how it skews the data. I actually think loan repayment is probably the more interesting metric - have others in your income class been able to repay their debts? You're also right that this tool doesn't help people see that choosing college A over B because of a $X,000 delta in average salary isn't a good idea as it's subject to all sorts of personal decisions.
3. This is really cool not because the tool is perfect, but because the government is releasing an API to go along with this - a number of private companies and non-profits have already integrated the data into their tools. This data, which hasn't been possible to get before, can now be integrated into the tools that were helpful to you (the ones that calculate in-state tuition, and ask you for sat/act scores). The underlying API also has many more data fields than the tool exposes. If fact, you can build one yourself! (https://api.data.gov/signup and https://collegescorecard.ed.gov/data/documentation/)