He does sometimes, like in Have I got a deal for you and Store 23 but sometimes he doesn't when he should, like in Fight at the Museum when he turned into Walkatrout. Like what R&CFOREVER said, the real world explination is because they want to make it more like the original series, and because necessity of plot, but an in-universe explination might be because it drains the power faster. I know that he said that a few times in AF and UA.
In-Universe explanation is that he usually gets knocked out of his alien form in like a minute because he randomizes the time-out by slamming his Omnitrix too hard. Also in Alien Force, it seems that his Omnitrix (Original) drains faster as well as shown in Darkstar Rising where after transforming from Echo Echo to Spidermonkey to Jetray to Humungousaur to chain combo Darkstar alongside Kevin, he already was out of his Omnitrix transformation.
The same is shown in Good Copy, Bad Copy where Ben fought Albedo for less than three minutes, constantly switching and after transforming into Chromastone for about one-two seconds, he already was reverted out of his transformation. Azmuth even said "those nonstrop transformations are going to break it".
Real World Explanation is that Ben was extremely overpowered with Quick Changes as seen in Darkstar Rising where he literally destroyed Darkstar with Kevin and Gwen's help which shows the full extent of what quick-changing with the Omnitrix can do, so they just dumbed it down for plot convenience and to give other Aliens more screentime.