You can't compare apples to oranges. The CBS 125 is faster because it was mechanically and by tune a much different motorcycle. Similar to how the Grom and Super Cub are faster than the Trail 125, the CT125 is tuned for mid range torque at the expense of top speed and peak horsepower. You're lucky to see any more than 45mph on a CT90, while I regularly cruise at speeds higher than that on my CT125. Consider the break-in of the CT125 if you aren't already past 600 miles, it does liven up a bit after that 600 mile oil change. After break in if your CT125 can't make it past 40mph then consider conditions such as if you've changed gearing, tires, elevation, how much you weigh, or if there might be an actual issue with your bike in particular. I just cleared 50 mph (GPS) on mine on an urban ride at ~5,000ft elevation picking up a sandwich for lunch today, and mine has a stock engine. Though there are mods such as exhaust, mine ends up being heavier than stock due to all the touring accessories I have on it.
I agree 2-strokes are wicked fun though. The most fun you can have on 125cc is probably with a 2-stroke 125cc. I had a Cagiva Tamanco 125 before the Trail 125 and it was lighter and much faster since it was 2T, but it was also a rare antique and nearly impossible to get some parts for in the USA, so it wasn't practical to rack up miles on.
If you want something fast, there are bikes from other brands that are different and faster with more guts. The Yamaha WR125R will likely even out perform the CT125 in that regard. Keep in mind the Trail is just a Honda Super Cub/Wave variant oriented for mixed use on and off road, and its primary market is Japan with 60kph (~37mph) roads where it shines.