Hi,
well, it's an open discussion, so take my point of view as it is: a point of view.
Separate clusters are pointless (in my opinion) because they'll not give you more info than one cluster.
They'll sense different things (otherwise they'd be spatially overlapped) and they'll not send infos to each other (better, probably they don't). I assume they all send data to a common server.
As a consequence, more cluster are good "only" to evaluate the effect of massive sensing over the common part: the server.
However, the very same analysis can be carried out by studying a single cluster, extracting the traffic patterns, and make a 2nd simulation with only a few nodes generating the aggregate traffic. It would be faster in this way.
Having different clusters will make your simulation more complex and, probably, harder to analyze.
KISS: Keep It Simple (and Stupid).
If the clusters can be overlapped... well, that would change everything. Some points in the overlapping case are:
1) the "clusters" are different PANs on different (non-interfering) channels ?
2) Why they're on different PANs ?
3) The sensing events are correlated ? E.g., you have a PAN for temperature and one for seismic events.
Anyway, I'd still study one PAN as a start.
Node failure... interesting topic, but you forgot one little thing... the routing :/ It's a multihop WSN, right ? Then you need routing, and that's even more important than the MAC. I'd say way more critical for the network resilience.
Simulation performance > translability > fidelity...
It depends on what's your goal. If you want to do a rough estimation with the simulator, and then move to a real testbed, then I agree that fidelity is the last point. However, you need some degree of fidelity. Otherwise your simulation could point you in the wrong direction.
I'd put the prios in this order: decent fidelity > performance > total fidelity > translability.
Translability is the very last thing you want, otherwise you should really consider Cooja or TOSSIM. The point is: a simulator goal (usually) isn't to be a rapid prototyping tool. You can, of course, check algorithms and write code in a way that leads to a minimal overhead translation, but NOT for WSN. WSN operating systems are so tiny, so limited and so specialized, that translating code is more difficult than to rewrite it. Otherwise you'll end up by using bad code in both cases.
One possibility to overcome this limitation is to use DCE (Direct Code Execution), but as far as I know DCE can't yet run Contiki or RiOT. Plus, as I said before... you should choose your OS because you want it, not because you're forced to use it by the simulator.
Summarizing, I'd not bother with translability. The simulator goal is to provide insights on the algorithm you develop, and to give you indications on what to do and what to NOT do. Once you know what's going on, the pitfalls and how to avoid them... rewriting code for the target platform is easy.
Cheers,
T.