If there is a possibility you might end up in house at some point, some companies are impressed by experience at large law firms, for some reason.
I'd say that the quality of the firm's clients is a more important factor than whether it is virtual or traditional. If they are doing work mostly for the large companies that lowball the fees, there is only so much they can pay you. Large companies are often the worst clients. The mid size companies that don't have in-house counsel usually are most satisfying to work for because they actually need and value advice, you are not just doing their overflow work. The largest companies tend to be more interested in numbers than quality.
For example, if they are doing 6k fixed fee patent applications for some large company that is more interested in numbers than quality, that limits what they can pay you. If they pay 50% (which is very generous), the most you could make is 3k per patent application. If they have good small clients that pay hourly or pay a higher fixed fee, the amount the firm can pay you is much higher. It doesn't matter what compensation plan they have if they don't have good clients. Keep in mind that some of the big names make the worst clients. I would ask all potential employers (assuming you have options) what their worst client pays per patent application. Then consider whether you really want to be in a firm willing to take on low paying work.
Another question is whether the virtual firm offers medical benefits, and, if not, if you can get insurance somewhere else.
Another thing to keep in mind is that when work gets tight, people who are present and on-sight are harder to ignore than people who are on the other end of the country. I would personally think virtual is better suited for more experienced people. If I were starting out all over again, I'd probably want to be located in Silicon Valley or Austin to benefit from good networking. If you end up in a city with a great quality of life (something virtual allows) but no alternatives than your virtual firm, it may be harder to jump ship if the work dries up.
Just some thoughts. Best of luck with your decision.