The problem is we still don't know what IAF is looking for. A strike aircraft like Rafale or air superiority like EF. We may never know because the shortlist seems to indicate IAF is fine with either.
I guess the IAF is fine with both aircraft for the following overarching reasons (beyond the detailed scoring in the RFP):
1) First they do not look at a single point in time (a sort of time freeze), but possess more than a well educated guess of the evolutionary potential of the two weapon systems. So one has to have a dynamic rather than a static frame of mind in trying to understand their rationale;
2) They consider both machines multirole, albeit with different areas of excellence;
3) Time will soon reduce these differences (the timeframe of operational significance for MMRCA is about 2018 + 35 years life). This build-up interval is small compared with the period of operational activity, say 2018 to 2050 with a centre of gravity around 2035;
4) In a force structure like the IAF with many types in service and under development, with overlapping capabilities in many combat mission areas, the risk of getting it wrong is much reduced compared to a single- or a two-type force structure. In this sense they are comfortable with both machines, and of course with their planned insertions of technology, capabilities and customization.
I would add as further observations what follows:
a) Rafale will never be able to perform in A-A against very high threat (I underline the threat aspect, because if you lower it then everybody performs) as Typhoon. This is mainly due to inferior specific excess power in the high supersonic regimes of modern BVR combat and inferior radar (size, power and scan volume);
b) Typhoon will expand its surface attack capabilities as per IAF agreed plans and basically match Rafale´s ones. There is absolutely nothing in its inherent design architecture that would impede it. Even its bigger re-positionable radar will contribute by delivering outstanding SAR imagery from high standoff ranges;
c) From 2025 onwards the A-G mission areas will gradually migrate to the unmanned platforms. So if you look at the long-term viability of your investment--and I guess that the IAF will have considered these aspects--the multirole fighter optimized for air superiority will make more sense.
d) Air superiority will remain also in the future the key pre-requisite for conducting a successful air campaign and winning a war. There will be no substitute for manned fighters in the MMRCA timeframe of reference.
These observations are of course of academical nature and a contribution to a civilized discussion, as the IAF has already made their choice (the two finalists) and it´s now up to the other constituencies to issue their verdict.