HE has over all a higher hull heal than ET. However, it is over time instead of instant. It also clears negative effects like plasma dots. Plus, if you use tac team or sci team, eng team will share a cooldown with those. My vote would be for HE.
One big advantage engineering team has over hazard emitters is that it'll bring damaged shields back up, say from a phaser proc or beam target shields. If you're fighting PvE this probably isn't a huge concern. Emergency power to shields has the same effect, but can onlly target you. (Engy team also counters VM and repairs other damaged subsystems, but shields down is the one that kills you.)
Hazard emitters, like the other dude says, counters some annoying crap, so it's sort of a tossup of what bothers you more.
Hull heals... can save you if shields are down, but it depends a lot on what you're fighting. Science ships of course have little hull to work with, unlike a cruiser. A high yield torp to bare hull isn't going to end well.
HE also has a damage resistance buff for its duration which can be rather significant.
I used to run all three teams when the doff system allowed you to stack Maintenance Engineers to reduce the CD of all the teams to 15s. At that time, given the option, I would use Tactical Team every single time until I had absolutely zero shields remaining in all of my quadrants.
You could make do with just HE as your hull heal, and for the majority of the solo content that's perfectly reasonable and doable.
Otherwise, Aux2SIF gets my vote for general hull heal. Weaker, but adds resists and has a short cooldown, doesn't interfere with my shiny tactical team.
I find that Aux2SIF actually heals for a little bit more than EngTeam with reasonable Aux power over the same period of time (Around 50 aux power is the break point IMHO) but it relies on the faster CD instead of a larger burst amount. Of course, running 2 copies of Eng Team will result in more healing per second, but that's two abilities compared to the one that also has the advantage of providing a hull damage resistance but without the repairing disabled/damage subsystems.
With max aux power, Aux2SIF provides for easily the same amount of overall healing as 2 copies of Eng Team.