I would say that it's definitely an individual decision. I enjoyed the corporate flying I did but there were a few problems with it for my long-term goals. I wouldn't mind going back to a large corporate flight department (and hope to do so), but I feel flying at a regional is currently more beneficial to my career and lifestyle
In a small flight department, you are only going to fly 200-400 hours a year, and when you are trying to build time to get that PIC job, that's not much. Insurance drives most corporate PIC minimums. To be insurable as a PIC on a turbine aircraft, you need in the neighborhood of 3000+ hours with a majority of it multi-engine, preferably turbine SIC. While a good corporate operator will hire a low-time copillot if they see them as trainable and they have a good attitude, you are going to be in an SIC position for many years. At the regionals, you will fly 600-900 hours a year depending on the schedules you fly. A potential drawback at the regionals is that your upgrade is soley based on seniority which may or may not be a bad thing depending on your airline. I know pilots that upgraded to captain in less than 6 months when a regional airline is expanding. However, at some regionals the upgrade time is indefinite meaning there isn't any movement - again, soley based on seniorty, not anything to do with your piloting ability or personality.
Another issue is schedule - most corporate jobs can't touch the schedule you'll have at a regional, in fact many corporate jobs have NO schedule. Granted, if you're only flying 200-400 hours a year, you are most likely going to be HOME more, but you don't have much control over WHEN you'll be at home. Reserve at a regional may not be so great depending on the airline, but even the most junior lines have a contract-stipulated minimum number of days off and you have control somewhat over what trips you want to fly and that control gets better each year you are there. Larger corporate operators tend to have more of a schedule, but in a smaller flight department, you can usually bet on being "on call" most of the time, even if it's not an "official" call-out period. Remember, the reason a company or individual has a corporate aircraft is so they can go where they want, WHEN they want, and not have to bother with the airlines.
Corporate pay will usually beat regional pay ESPECIALLY starting out. It really is embarassing what regional first officers make in their first year (been there). With corporate aviation, you also have the opportunity to negotiate raises, do extra work, and be creative in how you get the job done. In a smaller flight department you can count on having to do MANY other things besides flying the airplane. Each company is different, but you may do some (or all!) of the following - maintenance tracking, cleaning the aircraft/hangar, flight planning, catering, jepp updating, running errands for the boss, etc. You may go weeks without flying, but if you're on salary, there is ALWAYS something to do at the hangar.
I personally think that corporate aviation is much more challenging on the whole than the airlines and more satisfying. Corporate aircaft have much better performance than regional airliners on the whole. Ask many pilots who have flown many types of airplanes, and they'll tell you that once the excitement of flying a larger airplane wears off, an airplane is an airplane. Once airborne, flying is flying but with the airlines at the end of your day, the airplane isn't your problem anymore. At a large corporate flight department, you'll have a maintenance department and a director of aviation, etc. but at a smaller company, you may be everything! How are you going to get that major item fixed and still keep you job? Hopefully your boss has a realistic idea of how much it costs to operate his airplane, but many times you'd be suprised!
Job security: Corporate aviation - depends on the company. What if the company is sold? Will they keep your flight department? What if the boss dies and he was the only one in the company that is pro-aviation? If you're a corporate captain, you can step in somewhere else as a captain. Regionals - will I get furloughed? A 12-year regional captain who starts with another airline is now a 1-day first officer with the new company. Will the airline be sold and will I get "stapled" to the bottom of the new airline? Point is, nothing in aviation is 100% guranteed (ALWAYS have a "Plan B"). Of course, we all fly because we enjoy it - if you don't, you'll never make it in aviation.
When you're low time, ANY job flying a jet looks good (that's part of the problem with the regionals I feel). You still have to pay your dues in this industry and many guys don't fully understand that. Many guys look at all the advertisements in the flying magazines and see the high-dollar flight schools as an easy way to a jet-job, and it may be if you have the cash. It IS harder to pound the pavement, network, and find that corporate job, since many are word-of-mouth. If you show a genuine interest (assuming you can get your foot in the door) and have a good attitude, you'd be suprised what corporate opportunities are out there if that's the route you want to take. I'm proud of my time as a corporate pilot and hope to return to that kind of flying (in the right environment). However, I am still relatively low-time, married, and hope to have children soon, so I feel that my flying for a regional fits me better currently.
Both corporate and regional flying have plusses and minuses - you just have to decide which one is better for your long-term goals and what type of flying fits your lifestyle.