The biggest differences are history and money. Real Salt Lake as a team makes 3.5 million dollars, which is probably less than the average salary (or even the low salary) among the starting XIs of top European clubs (Madrid, Barcelona, Man U, etc). There are three individuals in MLS who make more than Real Salt Lake (Beckham, Henry, Marquez). As a team, Salt Lake would not rank among the top 20 salaries in Europe.
You can view all of the MLS salaries here in a PDF.
The history point is also significant and plays a part in the struggles that the US National Team has faced. A 12 year old academy player in Spain knows how his team is going to be playing when he's 20 and looking to break in with the senior squad and he knows how the Spanish national team will be playing when he's 22 and looking to break in there. A 12 year old in the US probably isn't part of an academy and is pretty much winging it with his development with hopes of going to a D-I college and then trying to break into MLS. If he's looking at how MLS looked 8 years ago and compares it to today and compares it to when he's 22 and looking to get drafted, it might as well be a different sport in many ways.
The roster restrictions are also significant. The kid in Spain I referenced will play with their youth side, then graduate to the B-side playing in meaningful league games, then move to the senior roster.
The kid in the US will bounce around youth and rec leagues, then high school and travel clubs, then college, then get drafted to MLS with different coaching and different systems to learn at every level.
Its really difficult to compare the leagues. MLS is much better than some of the Euro-snob crowd will give it credit for, but its also not competing with the top seven leagues in Europe in terms of overall quality. A good MLS match will be better to watch than a Stoke-Sunderland punt and run fest, but given roster restrictions it would be hard to see MLS teams surviving the drop in any of the top five leagues.
As for the Timbers playing Ajax, I wouldn't put much stock in the results. Portland is playing for pride and the legitimacy of MLS, while I'm not really sure what Ajax is doing playing a friendly in May. For what its worth, Kansas City beat Manchester United last season and then didn't qualify for the playoffs.