Eating too irregularly and having sudden peaks of glycemia/insulin can promote fat gain, but it depends on the context and it's typically a weak effect. What really matters for fat gains is whether there's a calorie excess in total on the whole day. Some people do "intermittent fasting" while being careful about the daily total and eventually they look rather healthy.
Another thing is that skipping breakfast will lower muscular protein synthesis and put you in a long catabolic phase, so that you will typically end up being less muscular. Having less muscles can also indirectly make you fatter, since muscles consume a lot of calories.
And a third point is that skipping breakfast makes you very inefficient during your morning, so it will reduce your NEAT, i.e. you will burn less calories than if you were able to stay more active physically and mentally.
Finally, skipping breakfast is usually correlated to taking less care about your nutrition, and this could bias the correlations that we observe from an epidemiological point of view. Because those correlations do exist, see for instance
http://jandonline.org/article/S0002-8223%2805%2900151-3/abstract "Breakfast eaters generally consumed more daily calories yet were less likely to be overweight" or
http://www.jahonline.org/article/S1054-139X%2806%2900264-3/abstract "Fast food consumption and breakfast skipping increased during the transition to adulthood, and both dietary behaviors are associated with increased weight gain "