I presume that the Mesa program is an FAR 141 program??? If so, is it self test, does it include multi engine training, and what are the total hours to complete the course?
Also, what is their average completion time for their students, historically? In other words, while the program takes XXX number of hours in terms of a perfect world, how many hours does the AVERAGE student actually usually complete it in?
Do you have access to a flight simulator? If not, all your instrument time will have to be in the airplane, burning $5 or $6 (or??) gas. Most 141 programs use simulators to reduce the costs to their students of the instrument training.
To complete Commercial certification under Part 61, the applicant must have completed at least 250 hours total flight time.
Under most Part 141 programs, a student can complete the commercial certification in 200 hours or less. In ours, a student can complete the commercial in as little as 170 hours, and most actually do so in less than 200 hours.
So, that guarantees at least 50 more hours of flight time to complete the Commercial if you "do it yourself", as opposed to a 141 program.
The multi engine training, which is pretty much mandatory for someone working in airline or corporate aviation, can be acquired separately, and perhaps even a little cheaper per hour, but don't forget that part of the training when you are doing the math.
I don't know about Mesa, but some college programs have access to more advanced training equipment as well, such as CRJ sims, etc. That sort of training can also be completed elsewhere, but....
My point is be sure to compare apples to apples if you are doing the math here. If you really compare one to the other fairly, there may not be that much difference, if any. In fact, in some cases, the 141 programs cost substantially less than a 61 program.
Finally, if you intend to work for the airlines, you need a college degree, regardless of where you did your flight training.
I believe that employers are going to look at where you completed your training, but it probably won't be a hire/don't hire kind of thing. There is no doubt that some of the bigger flight training programs in the country have good reputations, and employers are going to look at that.
So, in short, be sure you are making a fair comparison, and figure out what it's going to take to fill ALL the squares. Some of this the larger program can offer, whereas if you're doing it yourself, you'll have to go find those "add ons".
Finally, the flight instructor is HUGE in this kind of question. It can be hard to find a really good instructor, but if you know of one, and they'll stay with you through the course, great. Question is, what if they walk at mid stream? What if this happens three times? A larger flight training program SHOULD be able to fill in the "dissappearing" instructor with another fairly quickly, whereas if you're doing this on your own, this alone could be VERY frustrating.
Good luck.
MTV