Agreed that EK are excellent in the air. It's the DXB transits that are the problem, especially at night.
EK has 3 flights MAN-DXB but only one arrives during the day (0705). The others are 2000 and 0015. They have daytime connctions to some Indian destinations off that 0705 arrival but fairly longish transit times. My view on that would be make the most of it by getting a lounge pass and using those few hours to put our feet up. The transit then becomes bearable.
It really depends on your destination. A direct flight from the UK is invariably going to be better than a transit en route. Ultimately it will come down to personal choice (unless budget driven).
As far as visas are concerned, when I was going to India regularly (about 10 years ago) I must have had a multi entry visa valid for a year, as I only remember ever having to apply for a visa once amd I went at least 5 or 6 times (on LH). It's not fun - if possible get a visa agency to do it for you.