No one said that merging two of the biggest U.S. carriers was going to be easy; it isn’t. Frequent travelers who live near Northwest and Delta hubs might be excused for smiling as United and Continental travelers deal with some of the issues they dealt with a couple years ago.

The biggest issue right now is which airline’s equipment and crew is actually operating any given flight. The two airlines have been code-sharing for some time. Last year United began putting an asterisk on Continental-operated flights with United flight numbers. Anyone booking such a flight should have in theory seen a line underneath saying “operated by Continental.”

This year, many more flights have United flight numbers, but no asterisk. These flight displays say “Operated by United Airlines,” but still say in fine print, “check in with Continental.”

What does it really mean? For some travelers, the main potential hassle is when United and Continental gates and check-in kiosks aren’t in the same terminal or in the same gate area. There may mean some confusion at the airport.

In San Francisco, for example, the two airlines have moved to the same terminal, but they still use different gates.

The airlines are working diligently on changing this where it presents a problem. At most hubs both United and Continental are in the same terminal, but it’s good to double-check. (In Boston, at time of posting, the United uses Terminal C and Continental uses A.)

The bigger issues come with seats and upgrades. Again, the airlines are working on a more unified experience. But, they aren’t there yet. Any elite member booking a United flight and expecting the same automatic upgrade policy often will be disappointed.

Continental now upgrades United passengers automatically but only on the day of departure, if space is available; not the 48, 72, or 100 hours in advance Mileage Plus members might be expecting and are used to from the United side of the operations.

Plus, United has “Economy Plus” seating on all their planes. Continental does not. United has said they will start expanding Economy Plus to Continental aircraft in 2012.

In an attempt to offer a version of Economy Plus, Continental designates seats in the front of the economy class cabin as “premium seating” for elites. But there is a problem — the seats do not have additional legroom. The only seats with actual “extra legroom” are almost all exit rows, which are very limited. For the most part too, these extra legroom seats can only be purchased by non-elite passengers at time of check-in.

The differences in aircraft configuration doesn’t stop here. There are other differences between the aircraft. Continental has DirectTV on many of their planes (a pleasant surprise when we flew them in December); United does not. And the carriers’ food and entertainment options are still different.

Eventually all these details will be worked out. While “Economy Plus” will become the standard with the new airline, United has not announced what Continental features they might or might not keep. (Open note to anyone from United reading this, Direct TV is a big hit with every passenger I have talked to, even on a fee basis in Economy.)

For now, however, travelers who care about the differences should be particularly vigilant when booking United and Continental flights. Make any wishes known to travel arrangers or travel agents. While it may not be obvious at first, United is still noting when the the equipment used on different routes are operated and provided by Continental.

Going from memory or recent experience, on the other hand, is not enough. While frequent travelers may remember that flights in and out of Houston and Newark were old Continental routes and usually use those Continental equipment, United has switched equipment for flights from Dulles to Paris, Hong Kong to Saigon and even a flight from Chicago to San Francisco to Continental aircraft.

Finally, one thing will be certain in 2012 — whenever travelers get used to little steps in this merger, things will change. Stay tuned.