I'm not a HVAC professional, so take the following with the grain of salt. Having said that,
If the zoning controller is smart enough, it will be able to serve one room at a time to keep up with the demand, or balance the air distribution in such a way that the overall temperature will be just stlightly higher than the setpoint so you don't even notice. You'd be surprised what you don't notice - the temperature swings, as the A/C cycles, can reach 4-6F.
The perceived inability of your system tp do the job definitely has to do with the lack of balance - I was thinking the same thing before I started to catch up on HVAC, then it turned out that my unit was in fact oversized. It is not possible to reach the balance no matter how oversized the unit is - as johnl45 rightfully pointed out, you have a single thermostat, and it doesn't care. In fact, the more oversized it is, the less balance you have.
Another consideration is that you have a two-level - similar to what I have. To give you an example, before the zoning system was installed, the temperature difference was reaching 14F - how's that for a change? And, all the time one of the rooms (in the basement, facing north) had the register permanently closed all year round - it never needed extra conditioning.
I'd take a look at the insulation - just replacing the single pane windows and doors may be enough to bring the requirements 1 ton down, and that would be a better investment than a bigger A/C, and less expensive. Get the load calc done before you do anything else.
The only thing is - zoning systems are notorious for lack of information about them, and the usual tactics are to hard sell them on you in hope that you don't understand a thing and just go with the flow. I ended up with my own, cost me about $500, but this is not for everyone - it's rather an ongoing hobby than a solution, and R&D cost is not included 
Pros, correct me where I'm wrong.
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--vt
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