Hey Grakesh:
So I'll respond to the following setups you asked about, based on my experiences where applicable, and your desired price range of 3000-3500.
1. New Primaluna Prologue 3 preamp with Musical Fidelity A5 CR power-amp (New/Used).
-I've not heard the Prologue 3, and I've only heard the A5 with other MF gear, but wasn't blown away. I have to say that overall the new MF gear hasn't bowled me over the way the 308 or trivista stuff did. I think there are other SS amps I'd choose before the A5, Bat, plinius, and Sim being among them, especially with the forests.
2. New BAT VK-3iX preamp with USED Musical Fidelity A5 CR Power Amp
I've not heard these two together so I can't comment on the synergy, but it wouldn't be my first choice. Also, don't these two exceed your budget? Keep in mind you'll want to have some interconnects and PCs, so this might not be the way to go price-wise.
3. New BAT VK-3iX Preamp with USED BAT VK-250 / VK-350 power amp.
This is a much more logical combination than two IMO, but as far as I know there does not exist a BAT VK-350 amp, and the 250 used is still around 3500, which means you're way above teh budget listed above. Still, this would sound pretty sweet.
4. New Plinius 9200 Integrated
It seems based on other posts that you're leaning toward seperates, but I think the plinius 9200 is in some ways the ideal choice. It's got all the desired features (more than enough power, remote, phon section) and matches excellently with totem. I really think this is the winner, and the price used will leave you a nice amount left over for accessories or the bank (waste of time). If I hadn't blown an unnecessary amount of money on my seperates (I'm a schmuck) this woudl have been it.
5. New Musical Fidelity A5 Integrated.
I'm not in love with this integrated. I'm not anti MF, but I think the KW500 puts this to enough shame to make this one irrelevant. The tri-vista does for that matter too!
6. New BAT VK-300x Integrated.
Well there are really 3 different integrateds here: all SS, tube-hybrid, and tube-hybrid with supertubes. I loved the top of the line one with my totems, but the phono section is a bit of a joke. at the price used, though, you can get a good outboard phono stage.
7. Sim Audio I-3 / I-5 is another good choice. But I am not considring it highly because it is low on power amp portion and I want to use ths same set-up for powering my HT fronts as well.
Many have commented on this so I'll just say that I love the sim/totem combination and think you would be able to buy something used and resell it fairly easily if it didn't work out.
Okay, hope this helps. Again, I think considering your budget the best option would be the Plinius 9200. One not mentioned here would be the YBA passion integre, which is a killer integrated. Forget the power ratings...this one's a gem!