As bad as ALPA is for RJ pilots, it's the best of the bad options. For starters, look at the process for decertifying ALPA--it's deliberately difficult. Yes, USAir did it, but they had a very unifying cause in the Nicolau award to rally around, even though ALPA wasn't to blame. Further, for an R-ALPA to work, you'd have to ensure that every non-major would vote to decertify, essentially at the same time.
Second, in spite of Brand X's assertion that it would be easy to duplicate what ALPA does, the truth is, it won't be, and it won't be cheap. To wit, look at the recent vote by jetBlue. There was a strong push to go with an in-house union there, and one of the issues was cost. Granted, JB only had 2500 pilots at the time, but they all make more than regional pilots. If you had half the pilots making $100/hr x 1000 hours and half making $60 x 1000 hours, you'd have an annual dues revenue of $4,000,000 (assuming a 2% take). Out of that would have to come rent, insurance (corporate liability), assorted overhead costs...and that doesn't include full time employees, full time lawyers, a salaried President, a salaried VP and at least one salaried #3, and status reps, who would need to be pay-protected for lost time. Now, if all the regionals bailed at once, you might be able to double or triple the revenue, but I have no idea what those payroll values are. Cost was a major reason CAL rejoined ALPA.
Third, as was previously mentioned, you need career pilots, because you need people that are invested in the outcome. With so many pilots trying to get out, it will be hard to maintain continuity in leadership/management. Further, too many regional pilots just want to avoid rocking the boat so that they can get out....and that leaves senior pilots not only in charge, but driving the agenda.
Fourth, your airlines would have a field day testing out the resolve of a new union. At least today, they know what battles they can win. Imagine how slow the company would be to start turning over the dues money to a new union.
Fifth, don't discount what ALPA would do in retaliation. Most pilots aren't aware of the RJDC settlement (if you don't know what the RJDC is, do some research), which states that the major airline MEC is obligated to share its scope bargaining strategy with any ALPA regional that will be negatively affected. That allows--in theory--the regional to become a partner to the negotiations for DFR and job protection. It's obviously up to the regional MEC to enforce this, but the provision is there. If you vote out ALPA, ALPA will in turn do everything they can to hose you over even more--and win. Why? Because they have the resources and the power to do so. ALPA would only need to hold onto one regional, and those pilots would suddenly be getting super-preferential interviews/hiring via the major airline CBA's just to get revenge.
Finally, don't forget about the political side of things. The ALPA PAC would be able to grossly outspend a regional PAC, especially a new one, and that could lead to some negative ramifications. (Politics is also why the Canadian pilots have their own "office" within ALPA. Canadian labor law is different.)
Think of the sour regional/ALPA relationship as a bad marriage with money. If you're married to a rich person who's paying your bills and giving you some spending money, you can tolerate some philandering and embarrassment in exchange for the financial protection, at least until a better rich person comes along. The RJ pilots don't have a better rich person yet.
The better solution, working within ALPA, is for the regionals to try and force ALPA to adopt a bicameral BOD that would work like the two Houses of Congress: one "chamber" would be based on the size of the airline, and each would get so many reps, like the House of Representatives; one "chamber" would be based on the number of airlines, with each getting a single rep, like the Senate. When a policy is formulated in one chamber, it would not be allowed to go to the entire group or President until both chambers reconcile the language/policy. The current grouping practice needs to be replaced.
I don't enough about the ALPA Constitution and By-Laws or parliamentary procedure to know how this could be done, but it would be a better solution than trying to break away or start a new union, as it would keep all of the pilots in one union, and would force the union to truly represent the best interests of everyone.
And bear in mind that none of this address the most pressing problem of pilots willing to bargain against each other at lower prices to get the flying.