I am currently forced to rely on third party tools to handle combat because the encounters tool is so bad. So, here are my suggestions to make it better. 

First, let's talk about the positives: 

1. Very easy to set up and run an encounter. There's no fluff, just search the monster, add the party and start. All monster statblocks are present. 

My suggestions: 

1. Conditions. Conditions. CONDITIONS. Other combat trackers don't handle conditions well, and most of them completely ignore them. I'm not sure how this is not a day one feature, considering conditions are extremely necessary for combat.
2. Allow a "transform" button for Druids or other beasts, allowing them to change their HP and AC dynamically.
3. It would be pretty cool if damage types were automatically handled or gave us the option to handle them. 
4. Concentration reminders if a character takes damage while concentrating
5. Allow us to change the colors of monsters in a group. Personally I use digital assets in person, so throwing a color marker onto a token would make things so much easier.
6. Put a timer on a creature or character, reminding the DM "in two turns, this applies/no longer applies".
7. Allow DMs to adjust temp HP, AC, etc. Or at least give us a text box for notes.

I understand this is in beta phase, but usually after some measurable amount of time, improvements are made. I am relatively new to DnD, only playing for about a year, and I have seen nothing new come out for this tool. 

The three pillars of DnD: Social aspect, exploration, combat. One pillar is a complete PAIN to run because of this tool.