Speaking as someone who will probably get caught up in MTD sooner or later as they lower the thresholds, it's going to be a right p.i.t.a. At present, for our lettings business I use spreadsheets - just copy the template sheet each year that's pre-filled with 12 mortgage payments plus an entry for interest, 12 rent payments, entries for the annual insurance and gas safety checks, etc., and fill in the dates & figures every few months. I've got check calculations to spot if my double entries don't balance in a line, and space for the ad-hoc stuff. Then when everything's entered for a tax year, sort by date and there's all my transactions on one page - and totals at the bottom to copy onto my tax return.
For the last couple of years I've been using an online management package as I was expecting to be caught up in MTD by now. Guess what, I run the reports, then compare with my spreadsheets, then look for errors in the online system that cause it not to match - and yes, every time it has been the online system because it doesn't offer that "on a page" view and it's easy to miss something.
So assuming nothing else changes, it means the tax man actually gets less tax from me - I deduct the cost of the management software as a business expense. Assuming MTD doesn't change, they'll get 4 quarterly returns, but the figures will be total rubbish until I've sat down and done my annual "get everything up to date and do my self assessment" session.