Will my visa be approved or denied?

Hi! I just want to ask a question about my vusa application, when I was in Japan immigration advised me to get a COE for me to get a good visa since Im married with a japanese, and was advised that COE will be released around 2 to 3 months from the date of application,. So I went back to Philippines and sent all documents needed to my wife in Japan and she submitted it to the immigration office,. After 2 and half weeks I applied for a temporary visit visa since it has 90 days if its approved and was planning to just wait in Japan until my COE will be released, and luckily my visa wqs approved to stay for 90 days so I booked a flight a week ahead, however, 1 week before my flight my COE was released by the immigration in Japan and was sent to me which I received 3 days after the release date, so I went to Japan embassy to ask what to do, and embassy advised me that I should change my visa since I have COE, so I went to the same travel agency where I submitted my tourist visa and applied for a spouse visa,. Travel agency advised me that it will take a week or sometimes 2 weeks before it was approved by the embassy,. However its already 2 weeks and I havent received any text message or call from the agency, I called them multiple times but they just keep on telling me its still in the embassy and they cant say when it will be released or even denied.. Im getting worried and also keep on rebooking my flight which I found bery hassle for me.. can anyone educate me on whats happening with my application and why its taking long time for the result???

Takes much longer than 1 or 2 weeks. This is clearly a mistake by your travel agent.

Would have been better to get into the country, then do the process.

I'm a bit confused, maybe things are different in your country but, why is a travel agency handling your visa procedures? If you had a COE, and bring it together with your passport to the Japanese embassy, then you can get the visa stamped on your passport directly from them. Right?

Weird you are using a travel agent for a spouse visa application? Once a CoE is issued, the visa process at the embassy should be quite quick (advice I received years ago from my home country embassy suggested around a week).