Replacement for the Due?

We've been using an Arduino Due for our project, we need it because of the ability to have so many interrupts (we need ~20). We've tried using a Zero, which works decent, but only has ~11 interrupts ( Zero claims it has more, but when I set up a test system I remember there was only ~11 that were actually unique, multiple pins trigger the same interrupt)

What other hobbiest microcontroller has lots of interrupts?

Yes, we could redesign the system to multiplex the signals and combine them into one interrupt channel, we've gone down that route a bit in the past and it was too complex. We're trying to measure laser pulses, so it has to be ridiculously fast so from our experiments it was easiest to just have individual interrupts. Also, if we redesign now, we need all new hardware and circuit boards, so thats a last ditch effort.

I didn’t think that the Due had any unique per-pin interrupts; only per-port “pin change” interrupts.
True, the “attachInterrupt” for Due supports that pin-change interrupts, and you have more choices about rising/falling/etc than on some other chips, and the ISRs are relatively quick thanks to the “clz” instruction that the CM3 has, but you may be looking for the wrong thing. (Zero should have 16, but perhaps not all on the “available” pins. And they’re slower - all handled by a single vector that loops through all 16.)

So … what’s wrong with the Due? Just concerned about it’s future?

The TI Tiva ARM chips (Supported by Energia, which is an Arduino IDE clone) look like they have interrupts on every pin, similar to Due… The TI “Tiva Launchpad” is a low-cost development board that can be used.

Yeah, the Due is fine for now but its getting harder to find.

Just curious, when you say "harder to find", do you mean official boards only or clones also?

Plenty of the clones to be found on eBay.

Rather a bargain at £10.50 too.

Clones are fine, but the other downside is the the Due no longer has library support so it would be good to go to a newer board with better software

I'm hoping that someone takes the new SAMD5x processor and makes a Due-sized board out of it (Adafruit seems to be committed to an Uno-size board, but unlike the SAMD2x the 5x comes in big packages as well.) It might not solve your interrupt problem, though. Like the Zero, it seems to only have 16 pin interrupts. (Hmm. I wonder if you could allow the same interrupt on multiple pins, and change the ISR code to differentiate?)

I'm hoping that someone takes the new SAMD5x processor and makes a Due-sized board out of it...

That might happen. In Adafruit's video on SAMD51, Limor Fried expressed her intention to use the 100-pin version to create a Mega sized board.