Hi Shingo,
I wanted to encourage you not to sit too long with your feelings of being overwhelmed. They probably come more from not knowing what to do or how you need to do it rather than from feeling depressed that you can't do it. Don't lose sight of what you can do - and if you had to make a plan to get to where you are now, without the benefit of skills you have now, you would then be overwhelmed too. You have learnt and got somewhere already - you will move on from here, too.
As a basic recommendation for a start, a good series of sight reading books should progress you through the most common patterns that you use to read music. If you start at a lower level in these books and work through them as quickly as you feel comfortable, they should help build your identification of patterns. But, don't just read through them - try and find the patterns they are rehearsing (rhythm, chord and pitch progressions).
Part of the skill is having a certain perspective about the music. I think that was what your teacher was trying to say - looking at how the black markings on the page actually form shapes that are then translated into actions and sounds. A struggling reader looks at one note at a time and reads A C E, etc rather than acting more intuitively.
Scales are only one type of pattern. They can help you read when you are playing from a particular key. If you are in C major, you anticipate that nearly every note you play will be a white key. If you are in G major, you expect to play F#. In a minor key, you expect to see accidentals. All this is a very basic level of reading, and I am guressing you are way past this. (It also helps if you see a long, straight ascending/descending section becuase it is probably the scale foundational to the piece)
Related to this is the harmony. If you are in C major, you might pass through A minor or G major (at a basic level). You would also expect to play chords from C, G, F and a. If you have learnt the chords for each key (you should look at I, V, and IV before you start playing a piece and think what shapes (inversions producing these) these chords might appear in). Harmony becomes more complex than this, but this is where to start. (You can get away with reading without a creative knowledge of cadences and things - but this knwoeldge also helps with interpretation and expression, so it is necessary to develop understanding eventually.) Reading harmonies is building the visual and what you will expect to see, and if you see it then knowing where to place your hands.
Other patterns are rhythms. You will find different common rhythms in different time signatures. Work out what these rhythms are. Different time signatures, music styles, compound or simple time, etc all influence the types of rhythm patterns you will meet. Start with simple time and look at what you often see in your music at your level. Write out these patterns and tap them. Get the feel for them when you are doing other things away from the piano. (Tap your feet, etc). If you can see the shape of a rhythm pattern, you don't have to count its details, it becomes automatic. (You do need to do some study and analysis here to find your patterns.)
The other is arrangement of pitch - related distances between the dots on the page and how that translates spatially. These are chords/inversions/arpeggios and common movements (like your 1st to 3rd). These common movements create visual patterns when linked together. There are some that are very common (such as 4 notes progresssing one at a time). These really common ones are like the simple words (like 'and'). You get so used to reading these words that you don't stop to think that is 'a', 'n', 'd' spells 'and' - but once you had to when you first started reading. Now you just know becuase that is what the shape means. This is what happens in music and what I believe your teacher was referring to. Sure, you come across new and complicated words that you have to sound out before you can read them - but once you have done that you recognise it the next time. If it's a while since you looked at it, it might need sounding out again, but it sinks in with familiarity.
So, if you aren't already doing it, look at your music as a flow of pitch direction and time rather than as individual notes with thier own time value. Identify hte shape of progression within each beat for a start. Instead of reading G A B C, read four notes ascending from G. Adjust this principle to whatever level you are playing and reading.
Hope this helps.