Before we are quick to dismiss the role of AIP in RAN, just have a look at this writeup.
SEA 1000 CONVENTIONAL AIR INDEPENDENT PROPULSION | Australian Defence News & Articles | Asia Pacific Defence Reporter
There is also a paper done by DSTO on this very issue. Would be most interesting to read it...
DSTO > Publications > The Stirling engine power source for advanced marine applications
BTW, the plug-in section for an AIP for Collins has already been thought of by DSTO. Don't think they have discounted this:
http://dspace.dsto.defence.gov.au/dspace/bitstream/1947/3828/1/DSTO-GD-0042 PR.pdf
(page 4)
The operational needs for the Collins are somewhat different than most of the AIP owners out there - traditionally the Australian boats have run long distances - even up to Russian harbours - most of the AIP fleet out there is devoted to shorter runs with more time spent defending or denying smaller tracts of water.
For them, a smaller, handier boat with lower endurance is a good tradeoff vs the benefits of AIP.
AIP is *not* a magic bullet - you're giving up space and weight for both the AIP system and the fuel/oxidiser which will allow the boat to run underwater for a fairly short time. Given the power output vs volume/weight ratio of the AIP unit, you'll see that they usually kick out around 40kw or so, which is not enough to charge the batteries while running at anything over a few knots.
Collins plugged in very large gensets to rapidly charge their batteries so they can run quietly and snort every so often, giving them a higher advance rate (the rate at which they progress towards their patrol area) than other SSK's - it's not a huge margin, 10 knots vs about 8, but much higher than an AIP boat, which is nearer 4 knots.
Once you're out of fuel and oxidiser, that AIP set is a large chunk of nothing useful. In the Collins, the area formerly reserved for the AIP set was given over to tasks felt more relevant (a lockout area for divers I seem to recall)
It's best you understand what the Collins were intended for, look at a map and see the distances involved for the boat to even get to the patrol area, before you start seeing utility in fitting AIP.
AIP gets you some relatively fast submerged speeds for a short period of time, maybe twenty hours or so at high speeds of 18 or more knots.. Maybe less.
That's no good for Australia and the ops it's tasking it's subs with.