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It is highly implied that Elise did indeed love Sonic throughout the storyline of Sonic the Hedgehog. Shown through Sonic's Trial of Love, a cutscene where Amy confronts Elise about her liking someone, and most controversially, a scene which Elise revives Sonic through the use of a kiss, telling Sonic to come back to "us".
In Sonic the Hedgehog 06, Princess Elise kissed Sonic so he could come back to life and gain his super form. In the cartoon series, Sonic and Sally kiss each other in the very last episode before the series ends. he kissed a lot! sally, elise, mina the moongoose (well actually she forced it but it counts) and Fiona the fox NN96
Sonic died in Sonic the Hedgehog 2006 when Mephiles impaled him with an attack from behind. But Sonic was brought back to life by Princess Elise and her wish on the Chaos Emeralds.
Possibly because after she called to the Chaos Emeralds to revive Sonic, the Emerald's power gave her the power to bring him back to life, and so, she did this by kissing him on his lips.
He dies because Mephiles wanted to unleash Solaris so he could destroy the dimension, so the only way of doing that is by making Princess Elise crying, so he killed Sonic by shooting a Chaos Spear at him (causing Elise to mourn over the dead hedgehog).But sonic soon gets revived by using the power of the Chaos emeralds.