Yeah, I agree there were very glarring structural similarities between the Boo and Cell arcs, also in how the stakes were raised with new adversaries, though that being a common element in many arcs of the series.
The main distinction I feel lies more in the characters of Boo and Cell. Cell is driven by a clear objective—achieving perfection—while Boo initially presents as a seemingly less serious threat, with a more whimsical demeanor (though yeah, like you said this seemingly less threat came with the androids in the Cell arc). Yet, the inherent evil within Boo, eventually taking center stage, created a more compelling villain dynamic than Cell showing up as yet another more elaborated creation of Gero. The Cell character was more intricately plotted, which even sparked numerous theories, especially concerning its timeline complexities. However, I feel the Boo character itself feels more authentic and engaging and its existence and the way it was shaped, particularly in its conclusion with Boo embodying pure evil and his Kaioshin's absorptions shaping his character, the Kaioshin being introduced as another element of surprise in the arc relating with Boo in a cool and imo well done way.
The introduction of fusion as a means of power enhancement was also arguably more creative, contrasting with the somewhat abrupt and outta nowhere existence of the RoSaT. However, Gohan's power-up through Elder Kaioshin did seem a bit contrived, kinda cheap, while in the Cell arc his training with Goku was more in depth, even though many feel his pacifism and lack of will to snap wasn't so much in-character or something that could be derived from him, much the same way Goku's pacifism in the Freeza arc also didn't tag along with him previously not caring about killing who was evil --- sparing Nappa being the first sign I guess.
The Boo arc also imo handled better Vegeta's development, while in the Cell arc he seemed a little distinct from the more meticulous one from the Freeza arc. It explored his struggle with the then perceived adapting to peace on Earth but being a more driven rivalry in a nice way. Vegeta's actions, initially perceived as reverting to his cold, ruthless nature, being actually driven by his complex rivalry with Goku and Goku's willingness to fight Vegeta understanding Vegeta's need to settle their rivalry and not Vegeta being a cold killer was a nice character dynamic between them that lacked through the Cell arc. Boo arc I feel also encapsulated Vegeta's evolution very well, culminating in his selfless act of sacrifice and then acknowledgement of Goku --- with him noticing the contrast between the old Vegeta who should hate a Saiyan who is peaceful and fights for others... But without the hatred anymore, but an understanding of it -- was a significant moment of recognition for his character, affirming his status as a true Z warrior, though I'd say him attacking Cell when Trunks was killed and such being acknowledged by Piccolo in the end when he offered Vegeta a hand, being an, although implicit and not blatantly shown (which isn't bad, actually in many ways subtletie shows a better way of storytelling) cool coming from a previous villain who understood Vegeta well... which I can't take from the Cell arc, for it was well done.
Another worthwhile difference to me was the return of Goku as the central hero in the Boo arc, diverging from the Cell saga's focus on passing the torch to Gohan. While it was in line with the recurring theme of Goku as a protector, I prefer the way it ended in the Cell arc as a father passing to son the status with Gohan being introduced with an unparalleled potential finally paying off.
The introduction of characters Shin and Trunks had similar structural roles, though commenting on them, the depth with Future Trunks making a significant impact in the Cell arc, while Shin had potential but wasn't really well developed, going downhill in the spaceship had this potential in the Boo arc with Shin kinda downplayed, tho the Kaioshins as a whole still were essential for the arc in a way. Also, the dynamic between Goten and Trunks, as well as the unexpected depth added to Mr. Satan's character, enriched the Boo arc in this aspect as well imo. Mr. Satan's evolution from a gag figure, which was even in Boo arc's initial tune, to a character with a meaningful role, initially recognized by Piccolo as worth being helped for he tried to save the world his own way, was nicely and unexpected, ending with his big contribution in the final battle and family ties to Goku later on, contrasting with the overall gag and comedy relief he had in the CGs, like, who'd imagine that.
