I read everything I could find on this case over the past few days. It is a very interesting case and here are my thoughts on it.
I am 100% convinced Officer Ellis was targeted. I am also convinced his killer knew him very well. The killer placed an obstacle on the path Officer Ellis would take home when they knew he would be getting off work. The killer also knew him well enough to know, he would stop and move the branches out of the roadway. Officer Ellis was a very good officer and guy, they knew he would stop and move the branches. The killer also knew how deserted that exit would be at 2:00 am when Officer Ellis would be using it. It was 20-30 minutes after he was killed before the first cars used that exit. This also means the killer had a very good knowledge of the area and traffic patterns, especially at 2:00 am.
The murder weapon also has some interesting clues. It was a 12 gauge shotgun. Shotguns cannot be traced using traditional ballistic tests. They don't leave identifiable rifling markings like pistols and rifles do. Shotguns are also very forgiving when it comes to aim. A difficult shot at 30 yards with a pistol in the dark is an easy shot with a shotgun. The second part of the murder weapon I find important also relies on how accurate the reported news has been. According to multiple news reports, Officer Ellis was hit with multiple shots from a 12 gauge but with 2 different types of ammo. This could indicate a couple of things. Either 2 shooters, which is interesting since LE indicated they had evidence more than one person may have been at the scene when the shooting occurred, or a sloppy killer. Do we think it was a sloppy killer who didn't realize he had a mix of shells in his shotgun? No, because he was very clever in his planning and execution of the murder. He just didn't realize his idiot partner would have bird shot in his shotgun. Again, this part of my opinion relies heavily on the accuracy of what has been reported.
So, at this point I think Officer Ellis was killed by two people, who knew him, his schedule, the area at 2 am, and that shotguns aren't traceable by standard ballistic tests.
Motive is where this case will be solved if it is ever solved. The most likely motives in my opinion are:
1) Marital (Did she start dating anyone a few months later? I have no idea, it is just a question.)
2) Drug arrest related (certainly possible, but most drug lords/cartels understand how much heat murdering a pillar of the community cop would bring down. You go from a cop busting small time dealers to having the FBI, Secret Service, state police etc etc on every corner)
3) He knew something about a fellow cop and was gonna spill the beans. This makes the most sense to me. A fellow cop fits every criteria for this murder. They would know he would stop and move the stuff out of the roadway, that he takes that exit to go home, when he radioed dispatch to end his shift, that the exit would be abandoned at 2 am, and that shotguns aren't traceable.
I hope this case is solved but after 3 years, the odds are it won't be.
Don't forget that unless whoever it was intended to sit there all night, they had to know that he was on schedule to be at that place in a window of time. Having known and been around lots of LE and first responders, the first thing you learn is that just because someone's "shift ends" at a certain time, that certainly doesn't mean that they will be heading home at that time. They may have just made an arrest and spend hours completing paperwork and dropping off prisoners; they may have a sudden emergency at work that keeps them there for hours on end...
So whoever this evil killer(s) are, they were either a) willing to sit there all night (which must imply some urgency to getting the murder committed, right? as in, something is going to happen in the next day or two, or could happen any minute, that makes it worth sitting there all night; or b) knew that he was on his way home (e.g. from radio transmissions or other methods).