Change and Quake never went good together, the biggest negative effect of this in my opinion are the thousands of maps that never got played because of peoples unwillingness to change..
it was reflexs item timers that got me thinking about this, but as i read later, it wasnt an intentional change in gameplay... however it might be, i am a bit sad about this change, because i think it gave a lot of depth to the game.(not the math part, but how you had to orient yourself in time, between items and goals with the information you gathered, deducted, guessed)...
now again, i know that the item timers are a consequence of the new ui system, but many players have found sound arguments why they are a thing to keep. I think its mostly new players that like the new system because they havent been with the game long enough to really appreciate this element. It took me many years of playing to realy realy realize how strong positioning is.(think of how good strenx already was, but still cooller opened a whole new chapter in his playbook with his "know when to be aggressive and when to not be aggressive"... its the same with timing, you cant ever just learn it like a circle jump, there are just to many factors to consider to completely analyze even a short section of a duel game. No one can ever attain this perfection, thats why its beautiful because at times, magic happens and players reach towards this perfection.
Regardless of this i can see myself enjoying games with item timers, and just as you have fast maps like aerowalk, and slow like ztn, you could have maps with item timers and maps without them.
To give more examples; people go nuts over "small" changes like lowering the lg damage from 6 to 7, why not have them both? it was apparent very early in quake 3 that some weapons worked in duel but didnt have a desirable effect in tdm.
I dont think players would have such a strong resistance if the core gamplay stayed the same and give the mapers the power to incorporate the change where it is desired.
Mechanics such as the rocket and plasma ground boost which i really hope get added to reflex, would not appeal to everyone but im sure they wouldnt mind it if it was a map element, (map and area specific) and you could play maps with or without it.
The way it is with weapons basically, the mapper decides which weapons to include in his map
In short, dont change the core, instead introduce changes as map elements.