I'll have to agree with ehiney. This argument will bring out the pros and teh antis just like a Ford versus Chevy thread. There are a lot of pro-ETEC and anti-ETEC people. They have had a few issues (like just about any newer outboard), but they don't seem to have an inordinate amount. Mercury, Yamah, Suzuki, Honda etc. have also had issues. Honda seems to be in the lower half of that group as far as problem frequency. Perhaps this is because they were among the first companies to introduce 4-stroke outboards.
As far as real performance issues go. Two-strokes are generally lighter weight (ETEC=320lbs vs Honda=359-365lbs ). Not a huge difference unless it throws off the resting trim of your boat. Two strokes generally have a higher low end torque (and, therefore, low end thrust). This is evident in the ETEC vs 4-stroke video that everyone talks about. Whether this is really important tyo you depends on you boating situation. Noise is generally less in 4-strokes. Honda's extra weight (compared to some other 4-strokes) has been because they have added counter-rotating half-shafts (since their inception) that reduce vibration and therefore reduce noise. Honda is one of the quietest motors out there. ETEC is pretty quiet, too. Both are very fuel efficient. Both have good warranties and reputations of backing their motors (though Bombardier has been in the outboard business for a shorter time than Honda). The ETEC technology is not any older than the 4-stroke technology. They chose to go with different simpler injection technology than other injected 2-strokes, and seem to have fewer injection problems/failures as a result. 4-strokes require more maintenance, but no more than your (4-stroke) car.
You will have to decide whether you believe the internet noise about the two motors, then factor in the dealer service factor that ehiney mentioned and the cost (ETEC is generally cheaper). I recommend talking directly with owners of the motors rather than listening to internet. There are a lot of stories that start, " My Buddy...", " I heard...", or "The guy at the marina...". Some of these stories may be true, but a lot of them are actually third or fouth hand, rather than the first or second hand situations that they lead you to believe. There are also people whose warranty claims were rejected because they didn't meet the warranty criteria. Some are vindictive towards the company. I personally watched a guy try to restart his outboard after the computer shut it down because of insufficient water flow. I warned him not to do it. He ignored me and the results was a loud "bang" followed by the piston rod going through the block.
Take all of the info into acount and make your own decision.