For almost all Japanese sets UED is indeed rarer than 1st. For the E-series even way rarer. Expedition Base Set UED cards were only released as promotional releases, given at some events. How the UED Aquapolis and Skyridge sets were released I’m not sure, but those are way rarer than their 1st edition counterparts as well.
Here is a useful thread mentioning sets that were only printed in 1st editions; sets that were only printed in UED; and sets where UED is way rarer than 1st editions for the Japanese sets/decks: www.elitefourum.com/t/1st-edition-timeline-lets-iron-it-out/16054/1
And here a thread about the Expedition Base Set UED promos: www.elitefourum.com/t/japanese-unlimited-e-series-1-cards-base-expansion-pack/16426/1 Only the Ponyta is somewhat easier to find, because the UED came in a magazine. Most, if not all, of the other UED cards were only given at some events.
I’m actually still looking for the UED Expedition Base Pikachu in Japanese for my Pikachu collection (I do have the Skyridge UED one fortunately enough 
). The UED World Championship Pack Seviper and Battle Frontier cards are also the last two cards I still need to complete my Seviper collection… So yeah, UED are usually way rarer than 1st editions for Japanese cards.
Greetz,
Quuador