Would you buy your MB again?
This is a tough question. I've purchased a couple of bikes from them, my most recent being a Motobecane FantomDS Sport (which I actually got BD's sister-outfit Bike Island at an even greater discount).
I immediately started modding the bike and throwing money at it. Of course that was my choice, but if I had taken all the money I spent to upgrade and applied it to my original budget, I could have done pretty well.
The biggest issue is the way Bikes Direct markets bikes. Many (if not most) models have few photos, and the listed specs can be confusing and difficult to read. On the recent MB I purchased, I quickly discovered how the compromises made on the spec sheet made my upgrade path far more difficult than I anticipated (e.g. QR wheels paired with coil fork). The bike I recently purchased was far heavier than I anticipated; had I known this upfront, I probably would have kept shopping.
My primary bike is a Diamondback Catch 2 (also a direct-to-consumer brand). I do highly recommend Diamondback, for a variety of reasons. First, they are very affordable and you can get better deals than Bikes Direct if you google "Diamondback Corporate Discount" or have a Expert Voice account. Second, unlike Motobecane, Diamondbacks are shipped "Ready 2 Ride," i.e. they are super-simple to put together, they include all the tools you need, and they don't really cut corners on generic components. Let me give some examples--my Diamondback came with DB branded pedals and handlebar. Unlike nearly every other bike company, DB's stock pedals are actually good, flat pedals. Same with the handlebar--yeah, it's DB-branded, but it's perfectly fine and there's no compelling reason to swap it due to weight. They also included a DB shock pump with bikes that have air suspension--that alone saves you ~$35-$40. I could give even more examples. Comparing my experiences with Diamondback and Motobecane, Diamondback clearly wins on packaging, ease of assembly, initial experience.
I haven't purchased a high-end Motobecane, but it seems like they might be a better value than their low/mid-tier offerings. I'd still have a hard time recommending Motobecane to anyone who doesn't either work on bikes or have the finances to have it assembled/serviced.
I'd probably buy my Motobecane again, but mostly because I enjoy tinkering. But it's a close call--I literally spent hundreds of dollars on upgrades and that money would have bought me a lot more bike.