I have made multiple bookings using makemytrip.com during the past two years and here is my review.
1) Flights cost more than most of the other website. You are baited by giving a discount after the the price is increased but even after the discount you pay more than when booked on other website. I have always found some website cheaper than make my trip.
2) Hotels: Make mytrip.com always increases the hotel rates and then gives a discount which usually comes to nearly same as on other websites . But the hotels which are available on makemytrip.com are bad hotels which cannot sell their rooms because of poor quality and service . Again the worst rooms in those bad hotels are provided to make my trip customers.
3) I have never booked holidays using make my trip but my comparison has shown they are pretty expensive and poor quality compared to the money they charge. I have checked many packages and they seem very expensive and the hotels they provide in the packages are very bad. Now I have decided that I will book the hotels directly or the other option is to stay in a homestays which give a 5 star kind of facilities for much cheaper price. But there are some disadvantages also.
4) Train booking: I prefer to book train tickets using the make my trip as I hate the Indian Railways website. I pay an extra as an agent fee but its much easier to manage my trips. May be people who are used IRCTC.in may find it better.
This is one experience I had with make my trip when I booked a hotel.( I have booked hotels through make my trip many times)
I had made the booking from make my trip by paying full money. The hotel name is Hotel Aston in Kolkota. Just one days before my stay date, the hotel called me saying that they cannot give me the room as make my trip.com had not made the payment. Then I had to call makemytrip.com and they immediately said payment will be arranged. After some time the hotel called back again saying that they have received only the partial payment and they will not be able to give me the room till they receive the full payment. I called makemytrip.com again when they said everything has been settled and the room is confirmed.
Reaching the hotel at 11:45pm in the night the hotel asked me to make an extra payment for the room leaving me no option.
In conclusion my findings are, there is no advantage booking using makemytrip.com, but you spend extra.
Do some reserach and surely you will get atleast 10 -20% cheaper on other websites, the same what you are planning to book from makemytrip.
Thanks
Manmath