All completely subjective. On the few occasions I used 387s - a couple of times on GN and when they were on the MML, I found them to be comfortable, smooth riding units. The only poor journey I had on one wasn't the fault of the unit, it was when GN stoppers were 4 car on a Saturday and the unit was full and standing. I think your post falls into the "I don't like these units so I'll write a subjective post to justify my position" category.
Subjective to a point, but this doesn't invalidate stakeholder opinions. However saying they're rough riding isn't subjective - they are, which is something they share with the entire Electrostar family, to a greater or lesser extend depending on where you sit of course. This wouldn't be so much of an issue if the seats were softer and more appropriately angled and there weren't things like the fixed armrest to bang into.
For example, it's basically impossible to use a laptop on a 365 (tiny tables and bounces around/wobbles too much), and let's not forget how they turned into roasting sweat-boxes every heatwave.
I don't recognise this view of the 365s. Over 20+ years I've seen plenty of people using laptops on these trains, in both airline and facing seats, so to claim it's "impossible" simply isn't correct. I have occasionally used one and can't claim to have had any issue. You'd certainly be having issues using a laptop on the other 365 replacement, the 700s, unless fortunate enough to be able to secure a seat in first of course.
As for bouncing / wobbling around, can you elaborate? This certainly isn't something I recognise, and this includes their early days when there was still jointed track around. The 365 has an exceptionally smooth ride by any measure, and in the centre section between the doors has probably the smoothest and quietest ride of *any* EMU I've been on, especially 1/3 2/3 door stock.
As for air con, notwithstanding the possibility of retrofitting as was done by Chiltern in their similar 165s, personally I prefer the availability of all-year-round fresh air ventilation over air conditioning for the tiny handful of days where the weather is sufficiently warm (this year in particular it's probably been about 5 days at the most!). Given the current seating in the 387s and 700s, I'd very willingly trade air conditioning for more comfortable seating.
It's worth adding that the 365 is also more suited to commuter journeys than a 387, with a wider aisle but at the same time more seats. Ideal for the peak journeys they were deployed on.