There is indeed a fundamental difference.
The Brain-in-a-vat seems within the reach of even human technology. In other words, it is a highly convincing and realistic scenario. A brain in a vat would presumably take the simulated physical world to be the actual world.
The idea of a simulation, that the world itself, including the brain experiencing this world, could be a simulation is much more fantastic and therefore somewhat more difficult to accept as a possibility.
The main sticking point, however, is that we still have no explanation as to how our subjective experience could possibly be a property or consequence of the way our brain works. The idea of a simulation requires that we accept the idea that our subjective experience could possibly be a creation of the simulation and therefore, fundamentally, an illusion (see note).
In the Brain-in-a-vat, the nature, or indeed natures, of both our brain and our subjective experience remain exactly as each of us happens to believe that they are. With the idea of a simulation, both our subjective experience and the physical world are turned into illusions.
The Brain-in-a-vat, although more realistic and conceivable, is however entirely metaphorical in its motivation. It does not even try to suggest that you really are a brain in a vat. Rather, it is an argument, a logical argument, to help us understand why we cannot be certain of the reality of our perception of the physical world and, hence, of the reality of the physical world itself as we think of it.
The idea of the simulation is not an argument. It is a metaphysical claim about reality. A such, it is to be seen as connected with the idea that consciousness is a process and, therefore, to the idea that computers can become conscious. All that would be required would be that the software got to a sort of critical threshold of complexity.
The Brain-in-a-vat, on the contrary, suggests a decisive epistemological dualism between our own mind that we know, and that we therefore know that it exists (Descartes' "I think, therefore I am"), and the material world that we can only believe in, and that therefore we don't know that it really exists.
In effect, these two ideas are polar opposite. The Brain-in-a-vat says the physical world may not exist, while the simulation says that our subjective experience may be just an illusion.
To the extent that they are polar opposite, I don't see how anyone could see these two ideas as equally convincing. If you find them equally convincing, it is likely because you haven't understood at least one of the two.
The difficulty in believing in the possibility of our own consciousness being a simulation is that the only notion we have of what a simulation is comes with our notion of a material universe: we can only conceive of such a simulation as something of the same nature as that of a material universe. This is problematic for two reasons.
First, if the simulation was material in the same sense as that our material world, then we would be part of the material world of the simulation, which is definitely not what the idea of a simulation is meant to suggest to begin with. If instead the simulation was material in some different sense as that of our material world, then the notion of simulation becomes meaningless simply because nobody will be able to explain in what sense it would be material.
The second reason that it is problematic to believe in the possibility of a simulation of our consciousness comes from the fact that we are still unable today to explain the subjective quality of consciousness in terms on the material world.
A simulation, to the extent that we are only able to conceive of it as something akin to the material world, would be just as useless in explaining the subjective quality of consciousness. Merely assuming our material universe is a simulation fails to explain the facts of our consciousness.
In other words, the idea of a simulation doesn't make sense and doesn't explain anything.