Excellent question!
We bought our first house last year on a 3% down conventional loan. The property had been on the market for a while without much activity, so we made an offer at $5,000 (so 95k) below asking with paying taking 3% closing costs. We ended up knocking a bit off in inspection as well. The house was an estate and the family just wanted it gone. Knowing it was an estate, we wrote in that they could leave whatever personal property in the house that they did not want to move. At closing, the seller said that alone made them accept ours over others. The rehab was pretty easy and inexpensive, just many many hours of time in. We are listing that house in two weeks at 130k, meaning if we pay all realtor fees and closing costs we would walk away with approx. 30k.
The biggest adversity we faced is not having a lot of money to get started. We had just gotten married the month prior to buying the house, and paid for that in cash. We had to shop around until we found a good mortgage agent who was knowledgeable about options for low money down buyers. What I learned was mostly the process of buying a house and the importance of knowing as much about the property you're interested in as you can.
Best of luck to you in your future investing! I hope you'll be able to avoid some of the same pitfalls others have found.