The water main broke and flooded the entire basement and was never properly taken care of so I don't know if that would compromise the integrity of the structure.

That are *fairly* investor friendly (not as much as I'd like, but they suffice), and seem like the best compromise for a serious investor.That said, there are lots of options in this area -- just sit down with a bunch of brokers and ask questions.

In looking at the roof (I'm not a roofing expert) I know it will need new shingles, but there is also some wood rotting that I is visible from the outside, so I am hesitant that the frame under the shingles are also compromised. 

Can't hurt to ask your agent to request at least a partial release as a compromise!   

Or maybe you can't afford a huge turn key house in a good school district, but you could afford a small fixer in an decent district in the suburbs with a bit longer commute ... any way you slice it, the truth of the matter is that somewhere, somehow, compromises & sacrifices will need to be made in order to get you where you want to go, and only you can decide where and which sacrifices to make.Be wary of any person that tells you or method that looks like it requires no sacrifices ... that usually means you are missing some crucial information and/or there is some serious risk you are not seeing; there is no such thing as a free lunch, if it seems too good to be true, and so on and so forth.

@Ali Radhi If you are so desperate to start investing then you have to weight your options and compromise.

Compromise a little cashflow but really amp the returns? 

Replacing the microwave appears to be your least expensive upgrade IF you actually wanted appease your tenant with a compromise based on his requests.

 #2 is a good compromise, but there is another option IF you are planning on living in this house for at least a year.  

Unless the executor is drunk that day, or you have pictures of him in a compromising position, it ain't gunna happen.