Mani Dierseruvwe put Halifax in the lead before the hosts came back to win, although The Shaymen contributed to a fairly even contest for the most part.
"I really enjoyed it, I thought there were a lot of positives for us," Millington said.
"The result is obviously disappointing, and the manner of the goals we conceded, we were frustrated with.
"But all in all, it was a very good experience and there were a lot of positives from it.
"Out of possession we looked very solid for large parts of the game once we settled in.
"The lads are starting to build partnerships having been able to work together over a prolonged period of time.
"And in possession we looked like we carried a threat, certainly when we built play and when we countered, in both of those moments we looked like we had a threat going forwards."
When asked what he wants to see improved from his side, Millington said: "Everything that we did well today we can do better.
"But what I recognise is that with the point we're at in our pre-season, that was a good, solid performance and a good run-out against, certainly in the first-half, a very strong Fleetwood team."
Millington said his squad is where he'd want them to be at this stage of pre-season.
"Yeah, I'd like us to have a victory, but in terms of the fitness levels and the way we play, this was a marked improvement on Saturday," he said.
"It was a much more well-rounded performance in terms of being able to bring the moments of the game together, so it was very pleasing in that sense.
"If you think back to the Fylde game, it was purely about minutes and we hadn't done a great deal of work on things.
"There were, in some senses, aspects of our identity there, but over a longer period now, you're seeing more aspects of our identity coming out and influencing the game."
The Town boss says his squad will be ready for the start of the new season.
"I'm very confident, we've got a really good group of lads and a very strong group of footballers here," he said.
"Arguably, once we've got some more additions through the door, the strongest squad the club's had for a number of years.
"So it's very exciting and I'm really looking forward to Barnet."
Defender Jesse Debrah and midfielder Kian Spence were among those absent from the game.
"With Kian, the intention was always to ease him back in after last season, which was a gruelling season for him," Millington said.
"It was his first season in senior football where he played so many games at such a high level, and such a high intensity. Kian's a player who's often at the top end of the running stats in games, so last season was a real stress on his body.
"We knew it was going to take him time to recover and be available for us, and that's exactly what's happening.
"He's where we expected him to be fitness-wise, but there's certainly no intention currently of him moving on.
"And Jesse is the same. Unfortunately he's ill and has been for a few days.
"He's at home recovering in the club house, so he needs to get well.
"But I think we've shown we've got good strength-in-depth and there's players who can comfortably step in and do equally as well."
On Spence and Debrah's futures, Millington added: "I'm aware of interest from clubs, and they're not the only ones, we've got other players who other clubs have been watching, and will take an interest in because we've got a good group of players.
"But at the moment, there's no signs of them moving on."
On the other absentees from the Town squad, Millington said: "Sam, Matty Warburton, Luke Summerfield, Jordan Slew and Jordan Keane were all missing because they're at a stage of their pre-season where they didn't need the minutes.
"So they all took part in a training programme to maintain their fitness, and will all be present at one of the games on Saturday."
Read more from the Halifax manager later this week on our website and in Thursday's Halifax Courier.