It really does come to you for what's more important.
The 2016 MDX is in its third year and it's likely the reliability/quality is improved from the 2014's and 2015's. Not a valid sample size (but no one's anecdotal one is), but we had a 2014 loaner that had badly aligned panels. Inspected our 2016 like a hawk and it was way better. We don't have any odd noises from the rear suspension, and the transmission -- with the update already on the vehicle -- shifts fine for us.
That said, the Lexus's quality/reliability will still likely be better even if it's in the first model year of the new generation. Toyota/Lexus is probably the only brand nowadays that I'd trust for really high quality in the first year. Honda/Acura used to be great there but has clearly slipped.
We considered the Lexus as we don't really need the third row. So these are items from our situation:
- When we were purchasing, the Lexus had just came out and dealers were gouging. I'm sure now the prices are more reasonable. But you should get excellent prices on the 2016 MDX, in its third model year, and with the 2017 announced and supposedly shipping in the summer.
- The MDX isn't a sports sedan, but it still handles better than the Lexus, even in the F-sport incarnation. The trade-off is a firmer ride that only you can decide if it's worth it. Let's face it, some people enjoy the traditional Lexus ride -- soft, little feel, cushy. Others can't stand it.
- While the 2016 RX has improved cargo room, the MDX still kills it there. We take some cross-state trips and pack the vehicle.
- Power/acceleration on the MDX is noticeably better. It's not even that close. The Lexus is by our standards "adequate," but we like quick acclerations onto ramps, passing on mountain passes where we have to get into the oncoming lane.
- Styling on the MDX is okay to us, we liked it better than the 2nd gen with its more pronounced beak. The Lexus is controversial -- I can probably get used to it, my wife actually likes it.
- The luxury quotient on the Lexus is noticeably better. The cabin feels nicer, the MDX isn't bad but it's definitely a level or two below. Materials just feel better on the Lexus. That said, did you notice some hard dash pieces on the side of the steering wheel? Surprisingly cheap for a Lexus.
- The vehicle we really wanted was the XC90 Inscription. A lot of the positive assets of both except I'd never buy a first-year (and maybe second year) Volvo. (Then again it's probably gotten to the point where I wouldn't buy a first year Acura either!) But I doubt you'd be interested since you're looking for higher-end quality/reliability.
2016 MDX SH-AWD Advance
2006 Subaru Outback XT Limited
Departed: 2001 Acura MDX Touring, tranny died after 15 years, 120k miles