Thomas Jefferson wanted to see a more limited executive than we have today. He wanted a system in which a democratically elected Congress would have more power than the current Congress does. This system would have been more like that of modern Britain in which there is not an executive branch that is separate from the legislative.
Of course, there would be pros and cons to such a system instead of what we now have. On the pro side, such a system would be less likely to result in the gridlock that we currently see. We have a Congress that is part Democratic and part Republican with a Democratic president in the White House. What that has gotten us is a government that cannot agree on what to do in a time that seems to demand action. That is, one can argue, a significant drawback of our system. In that way, we could say Jefferson's system would have been superior.
On the other hand, Jefferson's system would not have offerred the same kinds of checks and balances that our system has. It would allow the government to act much more quickly, but that might not be such a good thing. Maybe it is better that we have a government that has a hard time acting quickly because that makes it harder for the government to do anything that is a really bad idea. In this way, you could say our system is better because it prevents the government from acting rashly.