Alija said he didn't wan't to separate BiH from Yugoslavia but if Croatia left then he didn't want Bosniaks to remain in a country that used to be equal among ethnic groups that turned into a country run by one ethnic group. Whether he was being honest here or not is based only on speculation. However, there was no evidence of Bosniaks preparing for war like there was in Croatia. It's not that they didn't wan't war it's that they weren't expecting it, but honestly if two republics already went to war to separate why would Bosnia be any different.

He also claimed that Bosnian muslims can't live with neither Serbs nor Croats so he propagated two possibilities: 1) Bosnia becomes an Islamic state with clear Bosniak majority (the goal he fought for from the start) and
2) He was ready to compromise- Bosnia is divided between the three ethnicities.
There have been released documents from the CIA regarding the break up of Yugoslavia stating what I have just posted. He knew there can't be an islamic state without kicking out the other two ethnicities. In his defense, leaders of all three nations had similar ideals. Serbs wanted to preserve Yugoslavia, the greater Serbia project (all Serbs in one country) came later when it was clear coexistance was no longer an option. Croats didn't want to stay in a country where Serbs dominated in both politics and military , while Serbs from Croatia didn't want to be a minority in a new Croatian country. I guess Croats should relate to Krajina Serbs somewhat.