There are a number of clues floating about that leave me optimistic we'll continue to see incremental additions to both the doe-2 engine and the eQuest interface in the future. Specific to VRF, note that DOE-2.1E functions have already been developed to directly model hourly behavior for a variety of VRF system setups [1] - I imagine it's a matter of time before such efforts get worked into something we can access directly via eQuest. I am not in a position to speculate or play up what may or may coming in the pipeline, but we have seen bits and pieces features under development surface over the past few years.
Advances are also still being made by others for simulation around the doe2 engine, outside of eQuest. At the last ASHRAE energy simulation conference, a platform-agnostic theme that kept resurfacing was how to go about tackling multi-variable "optimization" problems (and notably the "runtime" conundrum involved).
During the Lowdown Showdown presentations, team eQuest (disclaimer: I may have played a part in this) presented a unique doe-2 centric approach which, thanks largely to the raw speed of doe2 command line simulations (a benefit realized from decades of engine development, from an era when processing efficiencies were a necessity), was able to "brute force" a Monte Carlo simulation without the crutch/pitfalls of "seeded" genetic algorithms to inform simulations along the way. 24 design parameters were randomized and overnight produced a cloud of data from which we could identify a "first-cost optimized" minimal EUI result. In doing, so we did not just present the lowest EUI possible before adding renewables, but rather the best bang-for-buck combination of design parameters to suit an added "real world budget" constraint.
At present, I still consider the eQuest/doe2 platform my go-to choice for most simulation tasks. I recognize it isn't the best tool for every task, but that's why I carry more than one tool in my belt!
I'm confident we're going to see all of the tools in the playing field (old, new, and still unborn) make advances in years to come. It's an exciting time to be playing a part in the field of building energy simulation!
[1] EnergySoft - "APPLICATION FOR ADOPTION OF
VARIABLE REFRIGERANT FLOW
SYSTEMS UNDER THE TITLE 24-2008
NONRESIDENTIAL ACM PROCEDURES"