I expect the majority people with ILR will only hold it for 12 months before applying for British citizenship (which can take a few more months), so it isn't the end of the world. If you are at the front of the plane the non-EU queue may be faster anyway.
Not a fair assumption - there are many reasons why you might hold a foreign passport for an extended period of time, none of which are detrimental to the UK. e.g. I've had ILR for 38 years, and fully intend to live, work, invest, and be taxed in the UK for another 38 or more; I would dearly love to take up British citizenship, but my country of origin does not allow dual nationality, and the Home Office does not lie if asked, so what if I need to return for a "longer-than-tourist-visa" period for reasons outside of my control e.g. an elderly relative?
In my last 38 years of flying, I can count on one hand the number of times the non-EU queue is faster than the EU queue. Have you tried arriving back to LHR on a Thursday or Friday night? Or landing when you're not exactly the very first red-eye arrival of the morning? T5 at 11pm on a Friday night after a spot of wind, snow or rain makes MIA and ORD seem like child's play...
I'm not asking for special treatment, but (a) IRIS was efficient and not broke, so why remove it, and (b) why is the Registered Traveller Scheme open only to, errr, white ex-colonies and Japan, as opposed to ILRs who pay tax in the UK?