Your description reminds me of the Time Bokan Series, a group of anime series by Tatsunoko Production.
In all these anime series, there are similar characters:
- the main good guys are typically a boy, a girl and a talking animal/robot.
- the bad guys are typically a leading woman and two minions (a slim "tech" guy and a fat strong guy)
(there may be other supporting characters, e.g. a mentor for the good guys or an extra sidekick for the baddies, but they are not "mandatory").
Usually, both sides fight with mechas, often (but not always) animal-shaped and sentient:
- the good guys have typically a single robot or a limited choice of robots (e.g. they choose according to the terrain: a fish mecha for an underwater adventure, a bird if they need to fly...)
- the bad guys build a different robot every time, which is comically destroyed at the end of each episode (better if with huge explosion and nuclear mushroom)
Often the good guys recite a motto when they appear, sometimes mocked by the baddies. These characters and their funny quirks inspired many later anime characters, such as the bad guys of Nadia: The Secret of Blue Water (with inverted features for the minions: the slim one is strong, the fat one is the engineer) and Pokemon (Team Rocket are boy + girl + talking animal and they recite a motto).
The "Time Bokan Series" name comes from the first series, Time Bokan (i.e. The Time Machine), but the most famous and iconic of these series (at least in Italy where I live) is Yatterman. In this anime, the bad guys' symbol is a skull, so all their mechas have a skull painted somewhere (instead, the good guys' symbol is the letter "Y", which appears on the "good" mechas).
But, IIRC, the bad guys have a prominent symbol in others Time Bokan series as well.